Biomedical subjects

Yu Liu

Publications and source records attributed to Yu Liu.

At least 37 records · Page 2Linked to original sources

PubMed2025

The Genetic Basis of Elongated Tails in Birds: Evidence for Sexual Selection as a Driver of Convergent Evolution.

Elongated tails are exaggerated ornaments observed in various bird species, and their functional and evolutionary dynamics have attracted considerable attention. Empirical studies consistently show that sexual selection is a major drive of tail elongation. However, the genetic basis of this trait remains poorly understood. To address this gap, we performed comparative genomic analyses of 23 bird species, including 7 with extremely long tails and 16 with relative short tails. Genes related to feather development exhibited amino acid convergence replacement (e.g., APC) or displayed faster evolutionary rates (e.g., LEF1, WISP3) in the long-tailed species. Importantly, we identified convergence replacements of amino acids and rapid evolution in genes related to reproductive functions (e.g., PAQR7) and immunity (e.g., ADA), suggesting that elongated tails may serve as honest signals of genetic quality. In conclusion, this study provides genomic evidence supporting the role of sexual selection in the evolution of elongated tails, revealing an intricate interplay between sexually selected traits, fitness, and immune competence.

Animals↗

PubMed2025

Assessing the causal association between celiac disease and Alzheimer disease and frontotemporal dementia: A bidirectional Mendelian randomization approach.

This study aimed to investigate the bidirectional causal relationship between celiac disease (CD) and the risk of Alzheimer disease (AD) or frontotemporal dementia (FTD) using Mendelian randomization (MR), in order to clarify prior inconsistent findings. We analyzed summary-level genome-wide association study (GWAS) data for CD, AD, and FTD. Single-nucleotide polymorphisms (SNPs) strongly associated with each condition were selected as genetic instruments. MR analysis was conducted in 2 directions: from CD to AD/FTD and from AD/FTD to CD. Mendelian Randomization Pleiotropy RESidual Sum and Outlier (MR-PRESSO) was used to detect and correct for pleiotropy, and Cochran Q assessed heterogeneity. Leave-one-out and Mendelian Randomization-Egger (MR-Egger) regression sensitivity analyses were performed to evaluate robustness. No evidence of a causal effect was found between CD and either AD or FTD in either direction (P > .05). Similarly, genetic liability to AD or FTD did not increase the risk of CD. Sensitivity analyses supported the robustness of the results, showing no pleiotropy or heterogeneity. Our findings suggest that CD is not causally linked to the development of AD or FTD. While shared genetic factors or comorbidities may exist, the association is likely noncausal, and other mechanisms of cognitive decline in CD patients warrant further study.

Humans↗

PubMed2025

Modulation of Mettl5 alleviates airway allergy by regulating the epigenetic profile of M2 macrophages.

M2 macrophages (M2 cells) are known to be involved in both Th2 responses and immune regulation. However, the underlying mechanisms remain unclear. Functional abnormalities in macrophages are associated with airway allergy (AA). The objective of this study was to investigate the role of methyltransferase-like 5 (Mettl5) in macrophages and its potential to alleviate AA. In this study, an airway allergy (AA) mouse model was established using dust mite extracts (DME) as the specific antigen. M2 cells were collected from mice with and without AA. The role of Mettl5 in modulating the immune activities of M2 cells was assessed using both epigenetic and immunological approaches. We found that Mettl5 levels were elevated in airway M2 cells from mice with AA. The presence of Mettl5 in airway M2 cells was positively correlated with airway Th2 polarization in these mice. Airway M2 cells from AA mice exhibited impaired immune-suppressive function, which was resolved by ablating the Mettl5 gene in macrophages. Mettl5 was responsible for the hypermethylation of the Il10 promoter in airway M2 cells of AA mice. Exposure to DME induced Mettl5, which in turn recruited USP21 to deubiquitinate GATA3, thereby boosting IL-4 expression in M2 cells. Inhibiting Mettl5 restored the immune-suppressive capacity of airway M2 cells and mitigated experimental AA. In conclusion, Mettl5 plays a critical role in subverting the immune-regulatory capacity and enhancing IL-4 expression in M2 cells. Inhibition of Mettl5 can mitigate experimental AA by restoring the immune-regulatory functions of M2 cells.

Animals↗

PubMed2022

Temporal associations between leukocytes DNA methylation and blood lipids: a longitudinal study.

BACKGROUND: The associations between blood lipids and DNA methylation have been investigated in epigenome-wide association studies mainly among European ancestry populations. Several studies have explored the direction of the association using cross-sectional data, while evidence of longitudinal data is still lacking. RESULTS: We tested the associations between peripheral blood leukocytes DNA methylation and four lipid measures from Illumina 450 K or EPIC arrays in 1084 participants from the Chinese National Twin Registry and replicated the result in 988 participants from the China Kadoorie Biobank. A total of 23 associations of 19 CpG sites were identified, with 4 CpG sites located in or adjacent to 3 genes (TMEM49, SNX5/SNORD17 and CCDC7) being novel. Among the validated associations, we conducted a cross-lagged analysis to explore the temporal sequence and found temporal associations of methylation levels of 2 CpG sites with triglyceride and 2 CpG sites with high-density lipoprotein-cholesterol (HDL-C) in all twins. In addition, methylation levels of cg11024682 located in SREBF1 at baseline were temporally associated with triglyceride at follow-up in only monozygotic twins. We then performed a mediation analysis with the longitudinal data and the result showed that the association between body mass index and HDL-C was partially mediated by the methylation level of cg06500161 (ABCG1), with a mediation proportion of 10.1%. CONCLUSIONS: Our study indicated that the DNA methylation levels of ABCG1, AKAP1 and SREBF1 may be involved in lipid metabolism and provided evidence for elucidating the regulatory mechanism of lipid homeostasis.

Humans↗

PubMed2007

Fluorescence sensing and binding behavior of aminobenzenesulfonamidoquinolino-beta-cyclodextrin to Zn2+.

A water-soluble fluorescent zinc sensor which binds strongly to Zn2+ (log K = 12.4) was successfully synthesized under physiological conditions. This sensor exhibits a good fluorescence response to Zn2+ over a wide pH range in water. Under the same conditions, several metal ions commonly present in a physiological environment, such as Na+, K+, Ca2+, Mg2+, Mn2+, Fe2+, and Co2+, showed little interference to the fluorescence response to Zn2+. [structure: see text]

Binding Sites↗

PubMed2007

Mechanism of calcium accumulation in acetate-fed aerobic granule.

High calcium content has been widely reported in acetate-fed aerobic granules, but the reason behind this is unclear yet. By SEM-energy dispersive X-ray mapping analysis, this study showed that the majority of calcium was presented in the central part of the acetate-fed aerobic granule, and the granule shell part was nearly calcium-free. The elemental analysis of calcium ions coupled with the chemical titration of carbonate further revealed that the calcium ions that accumulated in the acetate-fed aerobic granule mainly existed in the form of calcium carbonate (CaCO3). The formation of the CaCO3 appeared to be highly dependent on the size of the aerobic granule, i.e., the CaCO3 precipitation was found only in aerobic granules with radiuses larger than 0.5 mm. These experimental observations with regard to the formation of CaCO3 in the acetate-fed aerobic granule were further confirmed by the model simulation, which was based on the principles of mass diffusion and carbonate dissociation in liquid phase. This study for the first time showed that the size of the acetate-fed aerobic granule would indeed play an essential role in the CaCO3 formation, and provided experimental evidence that a crystal CaCO3 core was not necessarily required for granulation.

Acetates↗

PubMed2007

Reversible 2D pseudopolyrotaxanes based on cyclodextrins and cucurbit[6]uril.

In this paper, a pseudorotaxane (2) was synthesized by reaction of cucurbit [6]uril with 6-[(6-aminohexyl)amino]-6-deoxy-beta-cyclodextrin chloride. Subsequently, pseudorotaxanes 2 were further assembled to form a 2D pseudopolyrotaxane (3) through an alpha,omega-PPG2000 diamino polymer threading the cavities of cyclodextrins in 2, and the resulting pseudopolyrotaxane was comprehensively characterized by FT-IR, NMR, TG-DTA, elemental analysis, and transmission electron microscopy. Significantly, the 2D pseudopolyrotaxane can turn into a main-chain pseudopolyrotaxane in the presence of base, and then the addition of alpha-cyclodextrins may result in a reversible switch between two different 2D pseudopolyrotaxanes.

Bridged-Ring Compounds↗

PubMed2007

Supramolecular assemblies of sulfonatocalixarenes with phenanthroline: factors governing capsule formation versus bilayer arrangements.

Four crystalline complexes were prepared by the inclusion complexation of the 1,10-phenanthrolinium ion (Phen) with p-sulfonatothiacalix[4]arene (TCAS) (2 from a solution at pH 1-2 and 4 from 1 M HCl) and with p-sulfonatocalix[5]arene (C5AS) (3 from a solution at pH 1-2 and 5 from 1 M HCl) upon varying the acidity of the solution. By combining the results obtained for complexes 2-5 with those for our previously reported complex (1), p-sulfonatocalix[4]arene (C4AS) complexed to Phen, it was revealed that p-sulfonatocalixarenes (CASs) form "bis-molecular" capsules (1, 2, and 3) around Phen at pH 1-2, whereas complexes 4 and 5 display distinct host-guest inclusion behavior at higher acid concentrations. The degree of compactness of the capsules increases with the enlargement of the calixarene cavity, which is affected significantly by both the penetration depth of Phen and the structure of the Phen dimer. Furthermore, the complexation behavior of TCAS/C5AS with Phen in 1 M DCl was investigated by using NMR spectroscopy, and was discussed in comparison with the previously reported results obtained from solutions at pH 2.0.

Journal Article↗

PubMed2006

TNF-alpha involves in altered prefrontal synaptic transmission in mice with persistent inflammatory pain.

Tumor necrosis factor alpha (TNF-alpha) is implicated in the development of persistent pain. Its expression increases both spinally and supraspinally after peripheral inflammation. The anterior cingulate cortex (ACC) is a forebrain structure known for its roles in pain transmission and modulation. Prefrontal synaptic transmission is potentiated in mice with chronic pain through an enhancement of presynaptic transmitter release. However, it is not known if TNF-alpha expression is altered in the ACC in response to persistent pain and if synaptic transmission within this region is modulated by TNF-alpha. In the present study, we examined TNF-alpha expression in the mouse ACC following hind-paw administration of complete Freund's adjuvant (CFA) and examined the role of TNF-alpha in ACC synaptic transmission. Quantification of TNF-alpha at the protein level (by ELISA) revealed enhanced expression following CFA-induced peripheral inflammation. In vitro whole-cell patch-clamp recordings revealed that TNF-alpha significantly enhanced synaptic transmission through increased probability of neurotransmitter release in the ACC. Our findings provide evidence that presynaptic alterations caused by peripheral inflammation is partly attributable to the up-regulation of TNF-alpha in the ACC.

Animals↗

PubMed2006

Amino acids labeled with [99mTc(CO)3]+ and recognized by the L-type amino acid transporter LAT1.

We have synthesized amino acids conjugated at the alpha-carbon through an alkyl spacer to a small tripod ligand. The tripod coordinates to the fac-[M(CO)3]+ moiety (M = Re, 99mTc). Depending on the lengths of the spacers, these metal complexes with pendent alpha-amino acids are recognized and transported by the l-type amino acid transporter LAT1. The best result was achieved with a butyl spacer. The Ki value of the corresponding complex is comparable to that of the artificial amino acid BCH. Efflux of [3H]-l-phenylalanine shows that the labeled amino acids do not only bind to the transporter but are transported into the cells. These are the first metal-labeled small molecules which are actively internalized to the intracellular space.

Amino Acids↗

PubMed2006

PduL is an evolutionarily distinct phosphotransacylase involved in B12-dependent 1,2-propanediol degradation by Salmonella enterica serovar typhimurium LT2.

Salmonella enterica degrades 1,2-propanediol (1,2-PD) in a coenzyme B(12)-dependent manner. Previous enzymatic assays of crude cell extracts indicated that a phosphotransacylase (PTAC) was needed for this process, but the enzyme involved was not identified. Here, we show that the pduL gene encodes an evolutionarily distinct PTAC used for 1,2-PD degradation. Growth tests showed that pduL mutants were unable to ferment 1,2-PD and were also impaired for aerobic growth on this compound. Enzyme assays showed that cell extracts from a pduL mutant lacked measurable PTAC activity in a background that also carried a pta mutation (the pta gene was previously shown to encode a PTAC enzyme). Ectopic expression of pduL corrected the growth defects of a pta mutant. PduL fused to eight C-terminal histidine residues (PduL-His(8)) was purified, and its kinetic constants were determined: the V(max) was 51.7 +/- 7.6 micromol min(-1) mg(-1), and the K(m) values for propionyl-PO(4)(2-) and acetyl-PO(4)(2-) were 0.61 and 0.97 mM, respectively. Sequence analyses showed that PduL is unrelated in amino acid sequence to known PTAC enzymes and that PduL homologues are distributed among at least 49 bacterial species but are absent from the Archaea and Eukarya.

Acetates↗

PubMed2006

Controlled delivery of recombinant hirudin based on thermo-sensitive Pluronic F127 hydrogel for subcutaneous administration: In vitro and in vivo characterization.

Here we investigated thermo-sensitive Pluronic(R) F127 (PF127) hydrogel for the controlled release of peptide and protein drugs after subcutaneous injection, using an antithrombotic polypeptide, recombinant hirudin variant-2 (rHV2), as the model drug. The in vitro release experiment performed with a membrane-less model at 37 degrees C showed that the release of antithrombotic activity of rHV2 from PF127 gel followed zero-order kinetics and correlated well with the weight percentage of PF127 dissolved, indicating a dissolution-controlled release mechanism. The in vivo result obtained after subcutaneous injection of rHV2-loaded PF127 gel in normal rats demonstrated that PF127 gel improved the bioavailability, prolonged the antithrombotic effect of rHV2, and induced detectable plasma rHV2 concentration for a longer time in comparison with rHV2 aqueous solution. Differential scanning calorimetry, dynamic light scattering and Fourier transform infrared spectroscopy provided evidence of the interaction between PF127 and rHV2, but such interaction was unlikely to interfere the feasibility of this drug delivery system. Our current in vitro and in vivo study suggested that PF127 gel may be useful as an injectable delivery vehicle for peptides and proteins with short half-lives to prolong their therapeutic effect, increase their bioavailability and improve the clinic outcome.

Animals↗

PubMed2006

Overview of some theoretical approaches for derivation of the Monod equation.

The Monod equation has been widely applied to describe microbial growth, but it has no mechanistic basis and is purely empirical. Extensive efforts have been dedicated to develop theoretical approaches for derivation of the Monod equation, which can be classified into three major groups, i.e., kinetic, thermodynamic, and substance transport approaches. In this review, four representative approaches are thus discussed. Due to the fact that different assumptions are made in each approach, no universal physical meaning of the Monod constant (K (s)) can be revealed. However, it seems that the Monod constant would be free energy-dependent and have nonequilibrium thermodynamic characteristics.

Algorithms↗

PubMed2006

Biodegradability of extracellular polymeric substances produced by aerobic granules.

This study investigated the biodegradability of extracellular polymeric substances (EPS) produced by aerobic granules. Aerobic granules were precultivated with synthetic wastewater in a lab-scale sequencing batch reactor. EPS were extracted from aerobic granules and were then fed as the sole carbon source to their own producers. Results showed that about 50% of EPS produced by aerobic granules could be utilized by their producers under aerobic starvation condition. The average biodegradation rate of the granule EPS in terms of chemical oxygen demand was five times slower than that of acetate, but 50 times faster than that of nonbiodegradable EPS produced by aerobic granules. The nonbiodegradable EPS was mainly found on the outer shell of aerobic granule. EPS produced by aerobic granules basically comprised two major components, i.e., biodegradable and nonbiodegradable EPS. The biodegradable EPS could serve as a useful energy source to sustain the growth of aerobic granules under starvation. This study provides experimental evidence that part of the EPS produced by aerobic granules would be biodegradable, but only nonbiodegradable EPS would play a crucial role in maintaining the structural integrity of aerobic granule.

Acetates↗

PubMed2006

Formamide probes a role for water in the catalytic cycle of cytochrome c oxidase.

Formamide is a slow-onset inhibitor of mitochondrial cytochrome c oxidase that is proposed to act by blocking water movement through the protein. In the presence of formamide the redox level of mitochondrial cytochrome c oxidase evolves over the steady state as the apparent electron transfer rate from cytochrome a to cytochrome a(3) slows. At maximal inhibition cytochrome a and cytochrome c are fully reduced, whereas cytochrome a(3) and Cu(B) remain fully oxidized consistent with the idea that formamide interferes with electron transfer between cytochrome a and the oxygen reaction site. However, transient kinetic studies show that intrinsic rates of electron transfer are unchanged in the formamide-inhibited enzyme. Formamide inhibition is demonstrated for another member of the heme-oxidase family, cytochrome c oxidase from Bacillus subtilis, but the onset of inhibition is much quicker than for mitochondrial oxidase. If formamide inhibition arises from a steric blockade of water exchange during catalysis then water exchange in the smaller bacterial oxidase is more open. Subunit III removal from the mitochondrial oxidase hastens the onset of formamide inhibition suggesting a role for subunit III in controlling water exchange during the cytochrome c oxidase reaction.

Animals↗

PubMed2006

Neuronal activity in monkey primary somatosensory cortex is related to expectation of somatosensory and visual go-cues.

The present study was to investigate whether neuronal activity in primary somatosensory cortical areas (SI) differs when monkeys expect go-cues of different sensory modalities. Two monkeys made wrist extensions and flexions after steadily holding wrist at a center position. Movements were guided by increases in vibration to the monkey's palm (VIB), visual targets (VIS), or both in combination (COM). Neuronal activity recorded in SI during the early and late phases (i.e., the first and last 250 ms) of the instructed delay periods (IDP) were analyzed. Of 406 neurons recorded during all three paradigms, 263 (64.8%) showed significant changes in firing rates (FR) between the early and late IDP phases during either VIB or VIS trials and were selected for further analyses. The selected neurons were classified as VIB- or VIS-biased, depending on the paradigm (VIB or VIS) in which the greater FR changes occurred. Both increases and decreases in FRs were observed during the analyzed epochs. Most VIB-biased neurons showed the biggest FR changes during VIB trials and the least during VIS trials. Conversely, most VIS-biased neurons had the biggest FR changes during VIS trials and the least during VIB trials. For both VIB- and VIS-biased neurons, however, the FR changes were intermediate during COM trials. These results suggest that SI neurons play an important role in initiating/executing wrist movements. Neurons involved in wrist movements showed biases to the modality of cueing signals. Most SI neurons were biased to only one sensory modality. The expectation-related FR changes suggest different involvement by SI in movement initiation when tasks are guided by vibratory and visual signals.

Action Potentials↗

PubMed2006

Cu2{[18]ane-N6} complexes: structures, magnetism, and phosphate monoester binding.

A novel Cu(II)2 complex of the [18]ane-N6 macrocycle ([18]ane-N6 = 1,4,7,10,13,16-hexaazacyclooctadecane) was prepared from the reaction between [18]ane-N6 and Cu(II) salts such as Cu(NO3)2 and Cu(OAc)2. A structural study of the complex derived from Cu(OAc)2 (1) revealed a Cu(II)2 core encircled by a [18]ane-N6 ligand and two mu-O-OAc ligands. The facile replacement of mu-O-OAc by a phosphate monoester [PO3(OR)2-] yielded a number of bis(phosphate monoester)dicopper complexes with ROPO3(2-) as hydrogen phosphate (HPO4(2-), 3a), phenyl phosphate [PO3(OPh)2-, 3b], glycerol 2-phosphate [PO3(OCH(CH2OH)2)2-, 3c], alpha-d-gluocose phosphate [PO3(C6H11O6)2-, 3d], and dl-alpha-glycerol phosphate [PO3(OCH2CHOHCH2OH)2-, 3e]. Structural studies of compounds 3a-d confirmed both the retention of the Cu2{[18]ane-N6} core and a mu-O-PO3(OR) coordination mode. Displacement of acetate by a phosphate monoester in an aqueous solution was accompanied by a significant change in the visible absorption, which enables the establishment of relative association constants of PO3(OR)2- on the order of 10(4) in the unbuffered solution and 10(3) in the buffered solution (HEPES). Measurement of the magnetic susceptibility of compound 3a over the temperature range of 5-300 K and subsequent modeling revealed a weak antiferromagnetic coupling (J = -1.1 cm(-1)) between two Cu(II) centers.

Carbon↗

PubMed2006

Alpha-actinin 4 potentiates myocyte enhancer factor-2 transcription activity by antagonizing histone deacetylase 7.

Histone deacetylase 7 (HDAC7) is a member of class IIa HDACs that regulate myocyte enhancer factor-2 (MEF2)-mediated transcription and participate in multiple cellular processes such as T cell apoptosis. We have identified alpha-actinin 1 and 4 as class IIa HDAC-interacting proteins. The interaction domains are mapped to C terminus of alpha-actinin 4 and amino acids 72-172 of HDAC7. A point mutation in HDAC7 that disrupts its association with MEF2A also disrupts its association with alpha-actinin 4, indicating that MEF2A and alpha-actinin 4 binding sites largely overlap. We have also isolated a novel splice variant of alpha-actinin 4 that is predominantly localized in the nucleus, a pattern distinct from the full-length alpha-actinin 4, which is primarily distributed in the cytoplasm and plasma membrane. Using small interfering RNA, chromatin immunoprecipitation, and transient transfection assays, we show that alpha-actinin 4 potentiates expression of TAF55, a putative MEF2 target gene. Loss of MEF2A interaction correlates with loss of the ability of alpha-actinin 4 to potentiate TAF55 promoter activity. Ectopic expression of alpha-actinin 4, but not the mutant defective in MEF2A association, leads to disruption of HDAC7.MEF2A association and enhancement of MEF2-mediated transcription. Taken together, we have identified a novel mechanism by which HDAC7 activity is negatively regulated and uncovered a previously unknown function of alpha-actinin 4.

Actinin↗