Biology subjects

He, M.

Publications and source records attributed to He, M..

At least 145 records · Page 8Linked to original sources

bioRxiv2020

Identification of Lysine Isobutyrylation as A New Histone Modification Mark

Short-chain acylation of lysine residues in eukaryotic proteins are recognized as essential posttranslational chemical modifications (PTMs) that regulate cellular processes from transcription, cell cycle, metabolism, to signal transduction. Lysine butyrylation was initially discovered as a normal straight chain butyrylation (Knbu). Here we report its structural isomer, branched chain butyrylation, i.e. lysine isobutyrylation (Kibu), existing as a new PTM on nuclear histones. Uniquely, isobutyryl-CoA is derived from valine catabolism and branched chain fatty acid oxidation which is distinct from the metabolism of n-butyryl-CoA. Several histone acetyltransferases were found to possess lysine isobutyryltransferase activity, especially p300 and HAT1. We resolved the X-ray crystal structures of HAT1 in complex with isobutyryl-CoA that gleaned an atomic level insight into HAT-catalyzed isobutyrylation. RNA-Seq profiling revealed that isobutyrate greatly affected the expression of genes associated with many pivotal biological pathways. Our findings identify Kibu as a novel chemical modification mark in histones and suggest its extensive role in regulating epigenetics and cellular physiology.

biochemistry↗

bioRxiv2020

An ancient deletion in the ABO gene affects the composition of the porcine microbiome by altering intestinal N-acetyl-galactosamine concentrations

We have generated a large heterogenous stock population by intercrossing eight divergent pig breeds for multiple generations. We have analyzed the composition of the intestinal microbiota at different ages and anatomical locations in > 1,000 6th- and 7th- generation animals. We show that, under conditions of exacerbated genetic yet controlled environmental variability, microbiota composition and abundance of specific taxa (including Christensenellaceae) are heritable in this monogastric omnivore. We fine-map a QTL with major effect on the abundance of Erysipelotrichaceae to chromosome 1q and show that it is caused by a common 2.3-Kb deletion inactivating the ABO acetyl-galactosaminyl-transferase gene. We show that this deletion is a trans-species polymorphism that is [≥]3.5 million years old and under balancing selection. We demonstrate that it acts by decreasing the concentrations of N-acetyl-galactosamine in the cecum thereby reducing the abundance of Erysipelotrichaceae strains that have the capacity to import and catabolize N-acetyl-galactosamine.

genetics↗

bioRxiv2020

Parabrachial neuron types categorically encode thermoregulation variables during heat defense

Heat defense is crucial for survival and fitness, and its dysregulation may result in deaths due to poor management. Transmission of thermosensory signals into hypothalamic thermoregulation centers represent a key layer of regulation in heat defense. However, the mechanism by which these signals are transmitted into the hypothalamus remains poorly understood. Here, we reveal that glutamatergic prodynorphin and cholecystokinin neuron populations in the lateral parabrachial (LPB) are progressively recruited to defend elevated body temperature. These two nonoverlapping neuron types form circuitries with downstream preoptic hypothalamic neurons to inhibit BAT thermogenesis and activate tail vasodilation, respectively. Both circuitries are selectively activated by warm temperatures and are required for fever limiting. The prodynorphin circuitry is further required for regulation of energy expenditure and weight homeostasis. Thus, these findings establish that the genetic and functional specificity of heat defense neurons occurs as early as in the LPB and uncover categorical neuron types for encoding two heat defense variables, which may provide targets for treating thermoregulation disorders.

neuroscience↗

bioRxiv2020

NMDA receptors require multiple pre-opening gating steps for efficient synaptic activity

NMDA receptors (NMDAR) are glutamate-gated ion channels that mediate the majority of fast excitatory synaptic transmission in the nervous system. A central feature of NMDAR physiology is the opening of the ion channel driven by presynaptically-released glutamate. Using glutamate applications to outside-out patches containing a single NMDAR in the continuous presence of the co-agonist glycine, we find that agonist-bound receptors transition to the open state via two conformations, an unconstrained pre-active state that can rapidly transition to the open state and contributes to synaptic events, and a constrained pre-active state that requires more energy and hence time to open and does not contribute to fast signaling. To define how agonist binding might drive these conformations, we decoupled the ligand-binding domains from specific transmembrane segments for the GluN1 and GluN2A subunits. Displacements of the central pore-forming M3 segments define the energy of fast channel opening. However, to enter the unconstrained conformation and contribute to fast signaling, a peripheral helix, the GluN2 pre-M1, must be displaced before the M3 segments move. This pre-M1 displacement is facilitated by the flexibility of another nearby peripheral element, the GluN1 and GluN2A S2-M4. We conclude that peripheral structural elements - pre-M1 and S2-M4 - work in concert to remove constraints and prime the channel for rapid opening, thus facilitating fast synaptic transmission.

neuroscience↗

bioRxiv2020

Elovl2 but not Elovl5 is essential for the biosynthesis of docosahexaenoic acid (DHA) in zebrafish: insight from a comparative gene knockout study

Teleost fish can synthesize one of the major omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFAs), docosahexaenoic acid (DHA, 22:6n-3), from dietary -linolenic acid (ALA; 18:3n-3), via elongase of very long chain fatty acid (Elovl) and fatty acid desaturase (Fads). However, it remains unclear which elongase is responsible for the endogenous synthesis of DHA. Here in this study, the knockout models of the two major elongases, Elovl2 and Elovl5, were generated by CRISPR/Cas9 approach in zebrafish and comparatively analyzed. The homozygous mutants were validated by Sanger sequencing, mutation-mediated PCR and whole-mount in situ hybridization analysis of the endogenous target genes. Compared with wildtype (WT) counterparts, the content of DHA was significantly reduced by 67.1% (p<0.05) in the adult liver and by 91.7% (p<0.01) in the embryo at 3 day-post-fertilization (dpf) of the elovl2 mutant, but not of the elovl5 mutant. Further study revealed that elovl2 and fads2 was upregulated by 9.9-fold (p<0.01) and 9.7-fold (p<0.01) in the elovl5 mutant, and elovl5 and fads2 was upregulated by 15.1-fold (p<0.01) and 21.5-fold (p<0.01) in the elovl2 mutant. Our study indicates that although both Elovl2 and Elovl5 have the elongase activity toward C20, the upregulation of elovl2 could completely replace the genetic depletion of elovl5, but upregulation of elovl5 could not compensate the endogenous deficiency of elovl2 in mediating DHA synthesis. In conclusion, the endogenous synthesis of DHA in is mediated by Elovl2 but not Elovl5 in teleost, and a DHA-deficient genetic model of zebrafish has been generated.

genetics↗

bioRxiv2020

Cascade Diversification Directs the Generation of Neuronal Diversity in Hypothalamus

The hypothalamus contains an astounding heterogeneity of neurons to achieve its role in regulating endocrine, autonomic and behavioral functions. Despite previous progress in deciphering the gene regulatory programs linked to hypothalamus development, its molecular developmental trajectory and origin of neuronal diversity remain largely unknown. Here we combine transcriptomic profiling of 43,261 cells derived from Rax+ hypothalamic neuroepithelium with lineage tracing to map a developmental landscape of mouse hypothalamus and delineate the developmental trajectory of radial glial cells (RGCs), intermediate progenitor cells (IPCs), nascent neurons and peptidergic neurons in the lineage hierarchy. We show that RGCs adopt a conserved strategy for multipotential differentiation but generate both Ascl1+ and Neurog2+ IPCs, which display regionally differential origins in telencephalon. As transit-amplifying cells, Ascl1+ IPCs differ from their telencephalic counterpart by displaying fate bifurcation to produce both glutamatergic and GABAergic neurons. After classifying the developing neurons into 29 subtypes coded by diverse transcription factors, neurotransmitters and neuropeptides, we identified their molecular determinants via regulon analysis and further found that postmitotic neurons at nascent state possess the potential to resolve into more diverse subtypes of peptidergic neurons. Together, our study offers a single-cell framework for hypothalamus development and reveals that multiple cell types along the order of lineage hierarchy contribute to the fate diversification of hypothalamic neurons in a stepwise fashion, suggesting that a cascade diversifying model can deconstruct the origin of neuronal diversity.

developmental biology↗

bioRxiv2020

Protein enhanced NIR-IIb emission of indocyanine green for functional imaging

Fluorescence imaging performed in the 1500-1700 nm spectral range (labeled as near-infrared IIb, NIR-IIb) promises high imaging contrast and spatial resolution for its little photon scattering effect and minimum auto-fluorescence. Though inorganic and organic probes have been developed for NIR-IIb bioimaging, most are in preclinical stage, hampering further clinical application. Herein, we showed that indocyanine green (ICG), an US Food and Drug Administration (FDA)-approved agent, exhibited remarkable amount of NIR-IIb emission when dissolved into different protein solutions, including human serum albumin, rat bile, and fetal bovine serum. We performed fluorescence imaging in NIR-IIb window to visualize structures of lymph system, extrahepatic biliary tract and cerebrovascular. Results demonstrated that proteins promoted NIR-IIb emission of ICG in vivo and that NIR-IIb imaging with ICG preserved higher signal-to-background ratio (SBR) and spatial resolution compared with the conventional near-infrared II (NIR-II) fluorescence imaging. Our findings confirm that NIR-IIb fluorescence imaging can be successfully performed using the clinically approved agent ICG. Further clinical application in NIR-IIb region would hopefully be carried out with appropriate ICG-protein solutions.

bioengineering↗

bioRxiv2020

An exploratory rehearsal on AIE dots assisted NIR-II fluorescence non-human primates imaging

Superb reliability and biocompatibility equip aggregation-induced emission (AIE) dots with tremendous potential for fluorescence bioimaging. However, there is still a chronic lack of design instructions of excretable and bright AIE emitters. Here, we designed a kind of PEGylated AIE (OTPA-BBT) dots with strong absorption and extremely high NIR-II PLQY as 13.6%, and proposed the long-aliphatic-chain design blueprint contributing to their excretion from animal body. Assisted by the OTPA-BBT dots with bright fluorescence beyond 1100 nm and even 1500 nm (NIR-IIb), large-depth cerebral vasculature (beyond 600 m) as well as real-time blood flowing were monitored through-thinned-skull, and noninvasive NIR-IIb imaging with rich high-spatial-frequency information gave a precise presentation of gastrointestinal tract in marmosets. Importantly, after intravenous or oral administration, the definite excretion of OTPA-BBT dots from the body was demonstrated, which showed an influential evidence of bio-safety.

bioengineering↗

bioRxiv2020

Effects of High-Grain Diet with Buffering Agent on the Milk Protein Synthesis in Lactating Goats

Feeding of straw as main roughage with numerous high-grain diets improves the performance of ruminants but it can easily lead to subacute ruminal acidosis. In recent years, buffering agent is applied to prevent the acid poisoning of ruminants and improve the production performance of ruminants in animal husbandry. it is necessary to understand feeding high-grain diet with buffering agent which transport carriers amino acids mainly take amino acids into the mammary gland and the signal mechanism of amino acids in the mammary gland synthesize milk proteins. To gain insight on the effects of a high-grain diet with buffering agent on the amino acids in the jugular blood, and the effects of amino acids on the synthesis of milk protein, commercial kit and high performance liquid chromatography (HPLC) were applied to determine the concentration of amino acids of jugular blood samples, quantitative real-time PCR, comparative proteomic approach and western blot were employed to investigate proteins differentially expressed in mammary tissues and the mechanism of amino acids on the synthesis of milk protein in mammary gland of lactating dairy goats fed high-grain diet with buffering agent or only high-grain diet. Results showed that feeding high-grain diet with buffering agent to lactating dairy goats could outstanding increase amino acid content of jugular blood (p<0.05), and mRNA transcriptional level of amino acid transporters in the mammary gland were also increased; the CSN2 and LF protein expression level were significant higher by 2-DE technique, MALDI-TOF/TOF proteomics analyzer and western blot analysis further validated in mammary of lactating dairy goats compared with high-grain group; the research on the mechanism of milk protein synthesis increasing suggested that it was related to the activation of mTOR pathway signaling. Feeding of high-grain diet with buffering agent promoted the jugular vein blood of amino acids concentration, and more amino acids flowed into the mammary. In addition, milk protein synthesis was increased and the increase of milk protein synthesis was related to the activation of mTOR pathway signalling.

biochemistry↗

bioRxiv2020

Genetic dissection of glutamatergic neuron subpopulations and developmental trajectories in the cerebral cortex

Diverse types of glutamatergic pyramidal neurons (PyNs) mediate the myriad processing streams and output channels of the cerebral cortex, yet all derive from neural progenitors of the embryonic dorsal telencephalon. Here, we establish genetic strategies and tools for dissecting and fate mapping PyN subpopulations based on their developmental and molecular programs. We leverage key transcription factors and effector genes to systematically target the temporal patterning programs in progenitors and differentiation programs in postmitotic neurons. We generated over a dozen temporally inducible mouse Cre and Flp knock-in driver lines to enable combinatorial targeting of major progenitor types and projection classes. Intersectional converter lines confer viral access to specific subsets defined by developmental origin, marker expression, anatomical location and projection targets. These strategies establish an experimental framework for understanding the hierarchical organization and developmental trajectory of PyN subpopulations that assemble cortical processing networks and output channels.

neuroscience↗

bioRxiv2020

Egg-surface bacteria deter oviposition by the oriental fruit fly Bactrocera dorsalis

Finding a suitable oviposition site is a challenging task for a gravid female fly, since the hatched maggots have limited mobility, making it difficult to find an alternative host. The oriental fruit fly, Bactrocera dorsalis, oviposits on many types of fruits. Maggots hatching in a fruit that is already occupied by conspecific worms will face food competition. Here, we showed that maggot-occupied fruits deter B. dorsalis oviposition and that this deterrence is based on the increased {beta}-caryophyllene concentration in fruits. Using a combination of bacterial identification, volatile content quantification, and behavioural analyses, we demonstrated that the egg-surface bacteria of B. dorsalis, including Providencia sp. and Klebsiella sp., are responsible for this increase in the {beta}-caryophyllene contents of host fruits. Our research shows a type of tritrophic interaction between microorganisms, insects, and insect hosts, which will provide considerable insight into the evolution of insect behavioural responses to volatile compounds.

ecology↗

bioRxiv2020

Association between ocular biometrical parameters and diabetic retinopathy in Chinese adults with type 2 diabetes mellitus

PurposeTo investigate the association between ocular biometrical parameters and diabetic retinopathy (DR) in ocular treatment naive patients with diabetes. MethodsThis cross-sectional study recruited type 2 diabetes mellitus patients with no history of ocular treatment in Guangzhou, China. The ocular biometrical parameters were obtained by Lenstar, including corneal diameter, central corneal thickness (CCT), corneal curvature (CC), anterior chamber depth (ACD), lens thickness (LT), and axial length (AL). The lens power and axial length-to-cornea radius ratio (AL/CR ratio) were calculated. Spherical equivalent (SE) was determined by auto-refraction after pupil dilation. Multivariate logistic regression analyses were performed to explore the associations of ocular biometry with any DR and vision threatening DR (VTDR). ResultsA total of 1838 patients were included in the final analysis, involving 145 5(79.2%) patients without DR and 383(20.8%) patients with DR. After adjusting confounding factors, any DR was independently associated with AL (OR = 0.84 per 1 mm increase, 95%CI: 0.74, 0.94), lens power (OR = 0.9951 per 1 D increase, 95%CI: 0.9904, 0.9998), and AL/CR ratio (OR = 0.26 per 1 increase, 95%CI: 0.10-0.70). Similarly, the presence of VTDR was independently related to AL (OR = 0.67 per 1 mm increase, 95%CI: 0.54-0.85), lens power (OR = 0.99 per 1 D increase, 95%CI: 0.98, 0.997), and AL/CR ratio (OR = 0.04 per 1 increase, 95%CI: 0.01, 0.25). The CC, corneal diameter, and refractive status were not significantly correlated with presence of DR or VTDR. ConclusionLonger AL, deeper ACD, higher lens power, and higher AL/CR ratio may be protective factors against DR. Considering the high prevalence of myopia in the Chinese juvenile population, it is worth paying attention to how the incidence of DR in this generation may change over time.

pathology↗

bioRxiv2020

The influence of insulin therapy on measurements of optical coherence tomography parameters in diabetic patients without retinopathy

PurposeTo determine whether there was a change in the fundus of the eye in diabetic patients without retinopathy after insulin therapy. MethodsThe diabetic patients without retinopathy were included in this study. A swept-source optical coherence tomography/angiography (SS-OCT/A) was used to obtain the measurements of macular retinal nerve fibre layer (mRNFL) thickness, ganglion cell-inner plexiform layer (GC-IPL) thickness, retinal thickness (RT), macular choroidal thickness (MCT), peripapillary retinal nerve fibre layer (pRNFL) thickness, peripapillary choroidal thickness (PCT), and perfused vascular density (PVD). Univariable and multivariable regression analyses were performed to explore the influence of insulin use on measurements of OCT/A. ResultsA total of 1140 patients used insulin (using group), and 126 patients did not use insulin (without group). The average MCT of the using group was 171.3{+/-}67.8 m, which was thinner than that in the without group (190.2{+/-}74.7 m) (P=0.012). The average PVD of the using group (48.0{+/-}2.1 m) was less than that in the without group (48.7{+/-}2.1 m) (P<0.001). After adjusting for age, gender, axial length, duration, HbA1c, systolic blood pressure, diastolic blood pressure, cholesterol, serum creatinine, insulin use was significantly associated with thinner MCT (beta=-16.12m; 95%CI:-29.42, -2.81m; P= 0.018) and lower PVD (beta=-0.79; 95%CI: -1.22, -0.36; P<0.001). ConclusionThe use of insulin by diabetic patients without retinopathy might decrease the MCT and PVD compared to patients who did not use insulin, which helps to better understanding the role of insulin use on higher risk for diabetic retinopathy.

physiology↗

bioRxiv2019

Primed acquisition and microhomology-mediated end-joining cooperate to confer specific CRISPR immunity against invasive genetic elements

CRISPR-Cas systems provide archaea and bacteria with adaptive immunity against invasive genetic elements through acquisition of invader-derived spacers. De novo spacer acquisition generally adapts spacers from both invaders and hosts with a bias towards invaders, while primed acquisition shows higher specificity to adapt spacers from invaders. Here, in Zymomonas mobilis subtype I-F system, primed acquisition showed much higher efficiency than de novo acquisition in this system. However, both routes recognised a large proportion of protospacers with the less conserved 5-end CC PAM. Moreover, primed acquisition showed a preference towards protospacers located at the opposite strand and 3 direction of the priming protospacer sites, differing from the canonical subtype I-F system. Further, self-spacers were adapted at a higher frequency during de novo spacer acquisition, probably leading to self-interference. Importantly, this species employed microhomology-mediated end-joining (MMEJ) for repair of host DNA breaks guided by self-targeted spacers, and overexpression of a host NAD+-dependent Ligase-A significantly increased the repair efficiency. In summary, our findings demonstrate that Z. mobilis uses primed acquisition for higher specific uptake of invader DNA and employs MMEJ to repair host DNA breaks guided by self-targeted spacers, showing specific immunity against invasive genetic elements.

genetics↗

bioRxiv2019

Nanog safeguards early embryogenesis against global activation of maternal β-catenin activity by interfering with TCF factors

Maternal {beta}-catenin activity is essential and critical for dorsal induction and its dorsal activation has been thoroughly studied. However, how the maternal {beta}-catenin activity is suppressed in the non-dorsal cells remains poorly understood. Nanog is known to play a central role for maintenance of the pluripotency and maternal-to-zygotic transition. Here we reveal a novel role of Nanog as a strong repressor of maternal Wnt/{beta}-catenin signaling to safeguard the embryo against hyper-activation of maternal {beta}-catenin activity and hyper-dorsalization. Knockdown of nanog at different levels led to either posteriorization or dorsalization, mimicking zygotic or maternal activation of Wnt/{beta}-catenin activities, and the maternal-zygotic mutant of nanog (MZnanog) showed strong activation of maternal {beta}-catenin and hyper-dorsalization. Although a constitutive-activator-type Nanog (Vp16-Nanog, lacking the N-terminal) perfectly rescued the defects of maternal to zygotic transition in MZnanog, it did not rescue the phenotypes resulting from {beta}-catenin activation. Mechanistically, the N-terminal of Nanog directly interacts with TCF and interferes with the binding of {beta}-catenin to TCF, thereby attenuating the transcriptional activity of {beta}-catenin. Therefore, our study establishes a novel role for Nanog in repressing maternal {beta}-catenin activity and demonstrates a transcriptional switch between {beta}-catenin/TCF and Nanog/TCF complexes, which safeguards the embryo from global activation of maternal {beta}-catenin activity.

developmental biology↗

bioRxiv2019

Sirolimus plus nintedanib treats vascular pathology in HHT mouse models

Hereditary hemorrhagic telangiectasia (HHT), a genetic bleeding disorder leading to systemic arteriovenous malformations (AVMs), is caused by loss-of-function mutations in the ALK1-ENG-Smad1/5/8 pathway. Evidence suggests that HHT pathogenesis strongly relies on overactivated PI3K-Akt-mTOR and VEGFR2 pathways in endothelial cells (ECs). In the BMP9/10-immunoblocked (BMP9/10ib) neonatal mouse model of HHT, we report here that the mTOR inhibitor, sirolimus, and the receptor tyrosine-kinase inhibitor, nintedanib, could synergistically fully block, but also reversed, retinal AVMs to avert retinal bleeding and anemia. Sirolimus plus nintedanib prevented vascular pathology in the oral mucosa, lungs, and liver of the BMP9/10ib mice, as well as significantly reduced gastrointestinal bleeding and anemia in inducible ALK1-deficient adult mice. Mechanistically, in vivo in BMP9/10ib mouse ECs, sirolimus and nintedanib blocked the overactivation of mTOR and VEGFR2, respectively. Furthermore, we found that sirolimus activated ALK2-mediated Smad1/5/8 signaling in primary ECs--including in HHT patient blood outgrowth ECs--and partially rescued Smad1/5/8 activity in vivo in BMP9/10ib mouse ECs. These data demonstrate that the combined correction of endothelial Smad1/5/8, mTOR, and VEGFR2 pathways opposes HHT pathogenesis. Repurposing of sirolimus plus nintedanib might provide therapeutic benefit in HHT patients.

cell biology↗

bioRxiv2019

Single Cell RNAseq Reveals A Critical Role of Chloride Channels in Airway Development

The conducting airway forms a protective mucosal barrier and is the primary target of airway disorders. To better understand how airway developmental programs are established to support air breathing and barrier functions, we constructed a single-cell atlas of the human and mouse developing trachea. In this study, we uncover hitherto unrecognized heterogeneity of cell states with distinct differentiation programs and immune features of the developing airway. In addition, we find ubiquitous expression of CFTR and ANO1/TMEM16A chloride channels in the embryonic airway epithelium. We show that genetic inactivation of TMEM16A leads to airway defects commonly seen in cystic fibrosis patients with deficient CFTR, alters the differentiation trajectory of airway basal progenitors, and results in mucus cell hyperplasia and aberrant epithelial antimicrobial expression. Together, our study illuminates conserved developmental features of the mammalian airway and implicates chloride homeostasis as a key player in regulating mucosal barrier formation and function relevant to early onset airway diseases.

developmental biology↗

bioRxiv2019

LncRNA GUARDIN suppresses cellular senescence through a LRP130-PGC1α-FOXO4-p21-dependent signaling axis

The long non-coding RNA GUARDIN functions to protect genome stability. Inhibiting GUARDIN expression can alter cell fate decisions towards senescence or apoptosis, but the underlying molecular signals are unknown. Here we show that GUARDIN is an essential component of a transcriptional repressor complex involving LRP130 and PGC1 which suppresses FOXO4 expression. GUARDIN acts as a scaffold to stabilize LRP130/PGC1 heterodimers and their occupancy at the FOXO4 promotor. Destabilizing this complex by silencing of GUARDIN, LRP130 or PGC1 leads to FOXO4-dependent upregulation of p21, thereby driving cells into senescence. We also found that GUARDIN expression was induced by rapamycin, a senolytic agent that suppresses cell senescence. FOS-Like Antigen 2 (FOSL2) acts as a transcriptional repressor of GUARDIN with increased levels in the presence of rapamycin resulting from downregulation of FOSL2. Together, these results demonstrate that GUARDIN inhibits p21-dependent senescence through a LRP130-PGC1-FOXO4 signaling axis and moreover, GUARDIN contributes to the anti-senolytic activities of rapamycin.

cell biology↗