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Yuqing Wu

Publications and source records attributed to Yuqing Wu.

16 recordsLinked to original sources
PubMed2026

Antibacterial and preventive effects of Terminalia chebula Retz. aqueous extract and methyl gallate in American shad Alosa sapidissima (Wilson, 1981) against Aeromonas hydrophila YML1.

American shad, Alosa sapidissima (Wilson, 1981), is an economically important emerging species in recirculating aquaculture systems and photovoltaic aquaculture. However, Aeromonas hydrophila poses a threat to the healthy development of its aquaculture industry. This study investigated the effects of 95.5 mg·L-1 aqueous extract from Terminalia chebula Retz. and 318.3 mg·L-1 methyl gallate (Experiment I) and methyl gallate at 31.8-127.3 mg·L-1 (Experiment II) together with A. hydrophila YML1 challage groups (1.0 × 107 and 1.58 × 105 CFU·mL-1 in Experiments I and II) on liver morphology, hepatic enzyme profiles, and transcriptional responses in American shad. Results for Experiment I showed after high-dose pathogen infection, vacuolar degeneration and inflammatory cell infiltration were observed. In addition, caspase-3, tumor necrosis factor α (TNF-α), and malondialdehyde (MDA) contents increased significantly, and the steroid biosynthesis pathway was significantly enriched via the transcriptional analysis. However, inflammation and apoptosis remained evident after high-dose A. hydrophila YML1 infection. After treatment with 95.5 mg·L-1 T. chebula Retz. extract, triphosphopyridine nucleotide (NADPH), Fructose-1,6-bisphosphatase (FBP), and phospho fructo kinase 1 (PFK) levels decreased significantly. After treatment with 318.3 mg·L-1 methyl gallate, nicotinamide adenine dinucleotide (NADH), NADPH, PFK, caspase-3, TNF-α, and MDA contents decreased significantly. For Experiment II, caspase-3 and TNF-α also decreased in the 31.8 mg·L-1 group at 24-96 h and in the 127.3 mg·L-1 group at 96 h. The peroxisome proliferator-activated receptor (PPAR) signaling pathway and fatty acid metabolism were also significantly enriched after methyl gallate treatment.Different expression genes (DEGs) in the cytokine-cytokine receptor interaction pathway showed a time- and dose-dependent pattern. At 48 h, the MAPK signaling pathway and apoptosis were enriched in the 95.5 mg·L-1 group, whereas at 96 h the PPAR-MAPK (mitogen-activated protein kinase) signaling pathway was enriched, with downregulation of fabp7b, soat2, cpt1ab2, and pparg. These changes were associated with inflammatory cell infiltration and increased MDA contents. Enhanced fatty acid degradation, possibly via cpt2, together with reduced fatty acid transporter transcription, may have alleviated liver injury in shad.

American shad↗
PubMed2026

NextLongIso: a comprehensive Nextflow pipeline for multi-dimensional long-read RNA-seq analysis.

SUMMARY: Long-read RNA sequencing technologies, including Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), enable direct characterization of full-length transcripts and transcriptome complexity. However, analysis of long-read RNA-seq data remains fragmented across multiple tools, limiting the ability to obtain a unified view of transcript structure, expression, and regulatory variation in long-read transcriptomes. We present NextLongIso, a scalable and reproducible Nextflow pipeline that enables coordinated analysis of multiple layers of transcript regulation. Rather than focusing solely on transcript reconstruction, NextLongIso integrates transcript discovery with downstream regulatory analyses to jointly characterize alternative splicing, isoform switching, transcript boundary dynamics (including alternative promoters and polyadenylation), and transposable element-associated transcription from both PacBio and ONT datasets. By eliminating complex cross-tool data harmonization, this unified framework facilitates the transition from transcript identification to functional interpretation of transcriptomic variation. AVAILABILITY AND IMPLEMENTATION: NextLongIso is implemented in Nextflow and is freely available at github: https://github.com/YidanSunResearchLab/nf-LongIso.git and Zenodo: https://doi.org/10.5281/zenodo.21049837.

Software↗
PubMed2006

Thermotropic mesomorphic behavior of surfactant-encapsulated polyoxometalate hybrids.

We investigate in detail novel organic-inorganic hybrid liquid crystalline materials, the complexes of surfactant-encapsulated polyoxometalate clusters (SECs), using thermal, X-ray diffraction, and FT-IR spectroscopic analyses. The differential scanning calorimetry measurements reveal four phase transitions under heating processes. We employ FT-IR spectroscopy to understand these phase behaviors. On the basis of vibration spectral assignments, the evidence suggests that the first two phase transitions are associated with the increase of gauche conformers and the disruption of alkyl chains packing in the heating run; the third phase transition is due to the full conformational disorder of alkyl chains covered on the polyoxometalates (PMs); no significant C-H stretching or wagging vibrations are observed with the fourth transition. We find that the fourth endothermic peak is sensitive to the charges of the PMs, and the transition temperature decreases from 185, 177, to 164 degrees C with decreasing PM charges from 13, 11, to 9, respectively. Interestingly, the temperatures of the first three phase transitions of SECs are essentially independent of the PM charges.

Calorimetry, Differential Scanning↗
PubMed2006

Enhanced expression of urocortin in lung tissues of rats with allergic asthma.

Bronchial asthma is defined as a chronic airway inflammatory disease characterized by sustained activation of many inflammatory cells including mast cells. Urocortin (UCN) is synthesized and secreted by human mast cells and activated mast cells release more UCN. On the other hand, UCN can induce mast cell degranulation and generation of many proinflammatory factors. The purpose of this study was to examine the expression profile of UCN in rat lung with allergic asthma. Twenty-four male Sprague-Dawley rats were allocated to normal control, asthma model, and dexamethasone group, respectively. Animals were actively sensitized by subcutaneous injection of ovalbumin (OVA) and challenged by an aerosol of 1% OVA 2 weeks after sensitization. Both UCN mRNA and peptide were expressed in normal rat lungs. Rats in asthma model group developed severe infiltration of inflammatory cells and inflammation in airway, together with a significantly up-regulated expression of urocortin mRNA detected by semi-quantitative reverse transcriptase-polymerase chain reaction and peptide measured both by immunohistochemistry and Western blot analysis. In contrast, treatment with dexamethasone resulted in markedly ameliorated airway inflammation and alleviated airway inflammatory cell infiltration, coupled with a significantly decreased urocortin expression. Regression analysis revealed a positive correlation between urocortin expression and the number of inflammatory cells in bronchoalveolar lavage fluid (P<0.01). In the present study, we first demonstrated that UCN was locally produced in rat lungs and expressed more pronouncedly in inflammatory airway of asthmatic rats. Glucocorticoid treatment markedly reduced the production of UCN in asthmatic lung tissues. Peripherally produced UCN in lung may act as a possible local autocrine and paracrine immune-inflammatory mediator in inflammatory airway of allergic asthma rats.

Actins↗
PubMed2006

Classification of the hydrogen-bonding species in a series of novel hydrazide based azobenzene derivatives investigated by two-dimensional correlation infrared spectroscopy and molecular modeling.

Classification of hydrogen-bonding species in a series of novel hydrazide modified p-methoxyazobenzene derivatives, 4-{n-[4-(4-methoxy-phenylazo)-phenoxy]-alkoxy}-benzoic acid hydrazide (Dn, n = 3, 6, 10) are performed in the present study. Temperature-dependent infrared (IR) spectra of Dn have been measured to investigate the thermal stability of the weak intermolecular interactions, such as hydrogen bonding among hydrazide moieties, pi-pi stacking among aromatic groups, and hydrophobic interaction between alkyl chains. In order to reveal the hydrogen bonding formed between NH, NH2, and CONH groups efficiently, two-dimensional (2D) correlation spectra have been constructed in the thermal sensitive spectral regions of (a) 3500-3100 cm(-1) and (b) 1700-1450 cm(-1), separately, and it have also been constructed between these two spectral regions. Based on the experimental data, the ab initio computational models have been developed to the proposed patterns of hydrogen bonding related to intermolecular interactions in Dn. The intermolecular hydrogen bondings and molecular alignments patterns result from both the experimental data and the computational models are performed for D3, D6, and D10, respectively, in the present study.

Azo Compounds↗
PubMed2006

Montelukast prevents the decrease of interleukin-10 and inhibits NF-kappaB activation in inflammatory airway of asthmatic guinea pigs.

Interleukin (IL)-10 is an important immunoregulatory and anti-inflammatory cytokine, whereas nuclear factor-kappaB (NF-kappaB) plays an important role in the pathogenesis of asthma. In the present study, the effects of montelukast on the level of IL-10 and on the activation of NF-kappaB in the inflammatory airway of asthmatic guinea pigs were investigated. Guinea pigs were sensitized by ovalbumin. Pulmonary inflammation was observed by hematoxylin and eosin staining. The eosinophils in broncho-alveolar lavage fluid and blood were separated by density gradient centrifugation and counted under microscope. The level of IL-10 in broncho-alveolar lavage fluid was measured by enzyme-linked immunoadsorbent assay. Activation of NF-kappaB in lung tissues was inspected by immunohistochemistry. Montelukast at medium and high doses prevented the decrease of IL-10 in broncho-alveolar lavage fluid (n = 8, p < 0.01 vs. asthma model group), inhibited the activation of NF-kappaB in lung tissues (n = 8; medium dose, p < 0.05; high dose, p < 0.01; vs. asthma model group). There was a significantly negative correlation between the level of IL-10 and the activation of NF-kappaB in lung tissues (r = -0.488, p < 0.01). Montelukast reduced the severity of airway inflammation and the number of eosinophils in asthmatic guinea pigs. From all these findings we conclude that montelukast can prevent the decrease of IL-10 and inhibit the activation of NF-kappaB in inflammatory airway of asthmatic guinea pigs, which may be the new important mechanisms of montelukast's anti-airway-inflammation effects in asthmatic guinea pigs.

Acetates↗
PubMed2006

Quadrature orthogonal signal corrected two-dimensional correlation spectroscopy.

Orthogonal signal correction (OSC) removes a substantial part of the spectral response that is orthogonal to the selected external variable. The combined use of OSC filtering and two-dimensional (2D) correlation analysis was proposed in the previous study (Wu, Noda, Meersman, and Ozaki, J. Mol. Struct., 2006, paper in press) to enable one to obtain high-quality 2D correlation spectra by eliminating any information unrelated to the external variables. However, the direct application of OSC to two-dimensional (2D) correlation analysis will result in the loss of the component that is significantly perpendicular to the external variable but also is the portion significant to the asynchronous 2D correlation analysis. Therefore, in order to avoid the problem of losing the valuable asynchronous 2D correlation information, the present study proposes a modified OSC filtering method, which is called quadrature OSC (QOSC) filtering. By replacing the external variable vector y used for OSC filtering with a two-column Y matrix consisting of y and its Hilbert-Noda transformation, the component of the spectral data asynchronously correlated to the external variable y is preserved. The performance of this technique on two simulated spectra data sets with a strong contaminant band and systematic noises has demonstrated that QOSC filtering 2D correlation analysis enables not only the elimination of the influence of signals that are unrelated to the external variable but also the preservation of the portions of information in the data matrix that are 90 degrees out of phase with y. It enables OSC 2D to deal with the problems of losing the portion of information that is perpendicular to the external variable y but is quite significant to the 2D correlation analysis.

Journal Article↗
PubMed2006

Expression of urocortin in rat lung and its effect on pulmonary vascular permeability.

Urocortin (UCN), a newly identified, 40-amino-acid, corticotropin-releasing hormone (CRH) structurally related peptide, has been demonstrated to be expressed in the central nervous system and many peripheral tissues of rats and man. This study aimed to investigate the expression profile of UCN in rat lung and the effect of UCN on lung vascular permeability. The expression of UCN mRNA was detected by reverse transcriptase PCR (RT-PCR). UCN peptide was measured by immunohistochemistry and Western blot analysis. We found that both UCN mRNA and peptide were obviously expressed in rat lung. Immunohistochemistry results showed that UCN peptide is mainly expressed in bronchial epithelium mucosa and alveolar epithelium. We also found that rats receiving inhalation aerosol of UCN had a significant elevation of lung vascular permeability compared with rats receiving vehicle and ovalbumin (OVA) by the Evans blue (EB) technique. UCN aerosol inhalation resulted in obvious pulmonary congestion and edema observed under light microscope by hematoxylin and eosin (HE) staining. The nonselective peptide CRH receptor antagonist astressin markedly reduced lung vascular permeability triggered by UCN. Enhanced pulmonary vascular permeability induced by UCN was markedly inhibited by pretreatment with the mast-cell stabilizer cromolyn and histamine-1 (H1) receptor antagonist azelastine respectively, but not by the leukotriene receptor antagonist montelukast. In summary, in the present study, we demonstrated for the first time that UCN is expressed in rat lung and contributes to an increase in lung vascular permeability through activation of CRH receptors. Mast cells and histamine may be involved in this effect of UCN. Peripherally produced UCN in lung may act as an autocrine and paracrine proinflammatory factor.

Acetates↗
PubMed2005

Urocortin reduces the viability of adult rat vascular smooth muscle cells via inhibiting L-type calcium channels.

The newly isolated peptide, urocortin (UCN), is a member of the corticotropin-releasing factor (CRF)-related peptides that has been found to have potent cardiovascular protective effects. In order to investigate the effect of UCN on the viability of adult rat vascular smooth muscle cells (VSMC) and the relevant mechanisms, we exposed the VSMC to UCN to observe the change in cell viability using MTT assay and intracellular calcium concentration using confocal laser scanning microscope methods. Our results showed that UCN (10(-7)M) inhibited the viability of VSMC by about 26% (P<0.05, compared to control). The effect was concentration-dependent, but it was not dependent on the affecting time. Glybenclamide (Gly, 10(-5)M), the ATP-sensitive potassium channel (K(ATP) channel) blocker, and astressin (10(-6)M), a competitive antagonist of CRF receptors, had no influence on this inhibition. Bay K8644 (10(-6)M), a special L-type calcium channel activator, increased the viability of VSMC. Pre-treatment of the cells with UCN diminished the effect of Bay K8644 (n=6, P<0.05). UCN was also observed to reduce the intracellular Ca2+ increase induced by KCl and Bay K8644. There was no significant difference in nitrite accumulation between UCN groups and the control. In conclusion, UCN reduced the viability of VSMC through L-type calcium channels. These interesting results might suggest that UCN may be a new vasoactive agent involved in hindering vascular remodeling in combination with previous reports about UCN's hypotensive effects.

Animals↗
PubMed2005

Effects of urocortin on T-type calcium currents in mouse spermatogenic cells.

Urocortin (UCN), a newly isolated peptide, has been found to play an important role mainly in female reproductive system. In order to investigate the effect of UCN on T-type calcium currents (I(Ca,T)), exploring the mechanisms of UCN's role in male reproductive system, especially in acrosome reaction, we directly measured the I(Ca,T) in mouse spermatogenic cells exposed to UCN using standard whole-cell patch-clamp recording technique. Our results showed that UCN reversibly inhibited the T-type Ca(2+) currents in the cells in a concentration-dependent manner. The current density was inhibited by about 19% after exposure of the cells to UCN (0.1 microM) for 5 min, from the control value of 6.75+/-1.17 to 5.26+/-0.82pA/pF. UCN up-shifted the current-voltage (I-V) curve. Frequency-dependence of UCN's effects on I(Ca,T) was also observed. Moreover, UCN at 0.1 microM did not markedly affect the activation of I(Ca,T) but shifted the inactivation curve of I(Ca,T) to the left. The inhibitory effect of UCN on the T-type Ca(2+) current was not affected by Astressin, the CRF receptor blocker. Since T-type calcium channels are a key component in acrosome reaction, our data suggest that UCN might be a significant factor in male reproductive action and a potential contraceptive agent.

Animals↗
PubMed2004

Structural and orientational studies of chiral N-[4(1-pyrene)butyroyl]-phenylalanine in cast film.

Cast films of chiral material N-[4(1-pyrene)butyroyl]-l-phenylalanine (Py-l-Phe) and the racemic modification (the 1:1 mixture of Py-l-Phe and Py-d-Phe) have been investigated in the present study. The microscopic structure, molecular orientation and the aggregation in the film have been studied by using ultraviolet-visible (UV-vis) and infrared (IR) spectroscopy. When a cast film is formed from the chloroform solution at room temperature, the J-aggregates of Py-l-Phe and Py-d-Phe are observed by UV-vis spectra. A comparison of Fourier transform infrared (FT-IR) transmission and reflection-absorption (RA) spectroscopy has been applied to reveal the orientation and structural characterization of the cast films. It has been found that the pyrenyl ring in the cast film of Py-l-Phe assumes a nearly vertical orientation with respect to the surface of the solid substrate. And there are two different hydrogen bonding species, cyclic dimer and linear dimer, exist in carboxyl groups in cast films. The detailed analysis of the OH and NH stretching modes of Py-l-Phe and Py-d-Phe allows us to reveal the hydrogen bonds existing in the films.

Chloroform↗
PubMed2004

Two-dimensional infrared spectroscopy study on phase transition and structural variations of a hydrogen-bonded liquid crystal.

Infrared (IR) spectra have been measured for a liquid crystal (LC) consisting of one trans-butene diacid (BD) molecule as a proton donor and two 4-(2,3,4-tridecyloxybenzoyloxy)-4'-stilbazoles (DBS) molecules as a proton acceptor (DBS:BD:DBS) linked together with each other by inter-molecular hydrogen bonds over a temperature range from 20 to 120 degrees C to explore its phase transition and heat-induced structural variations. The temperature-dependent IR spectra have shown that the inter-molecular hydrogen bonds are stable in the liquid crystalline phase but become slightly decoupled with temperature increasing. Two kinds of two-dimensional (2D) correlation spectroscopy, variable-variable (VV) and sample-sample (SS) 2D spectroscopy, have been employed to analyze the observed temperature-dependent spectral variations more efficiently. The SS 2D correlation analysis in the spectral range of 2700-1800 cm(-1) has demonstrated that a change in hydrogen bonds in the LC starts from 40 degrees C, which is not clarified by differential scanning calorimetry (DSC) and conventional IR and Raman spectroscopic analyses. On the other hand, the phase transition of LC revealed by SS 2D spectroscopy in the specific spectral regions of 1750-1650 and 3000-2700 cm(-1) is in a good agreement with that revealed by DSC for the heating process. The VV 2D correlation spectroscopy analysis has provided information about the structural variations of inter-molecular hydrogen bonds. The different species of hydrogen-bonded and free -COOH and -COO- groups in the LC have been clarified by the VV 2D correlation analysis. It has also elucidated the specific order of the temperature-induced structural changes in the intra- and inter-molecular hydrogen bonds concerning with the -COOH and/or -COO- groups in the LC.

Alkenes↗
PubMed2003

Raman spectroscopic investigation of the single-monolayer Langmuir-Blodgett film of C16NaphOH and C10AzoNaphC4N-SDS.

Raman spectra were measured for Langmuir-Blodgett (LB) films of C(16)NaphOH and C(10)AzoNaphC(4)N-SDS on Calcium Fluorite substrate for the first time. In order to find out favorable excitation condition, Raman spectra of the single and multi-monolayer LB films excited at different lines at 244, 514, 633 and 778 nm are recorded and compared in the present study. Raman spectrum of the monolayer LB film of C(16)NaphOH excited by 244 nm demonstrate that excellent signal to noise is achieved even for one monolayer LB film with an extremely short integrating time as 60 s because of being resonantly enhanced, while no meaningful spectra were recorded under the same condition for the monolayer LB film of C(10)AzoNaphC(4)N-SDS because of burning. Using a HeNe 633 nm excitation the problem with strong substrate fluorescence was partially solved, since under these conditions this fluorescence is mainly outside the fingerprint region of the LB film molecules (1000-2000 cm(-1)). Therefore by using the HeNe laser excitation, Raman spectra with high signal to noise ratio of LB films of C(16)NaphOH were collected and shown in this paper. These findings stress again the necessity to define an appropriate Raman system for this special application of LB film diagnosis.

Alkanes↗
PubMed2003

Two-dimensional infrared spectroscopy and principal component analysis studies on a new azobenzene derivative supramolecular system based on hydrogen bonds.

Infrared (IR) spectra of a supramolecular assembly with an azobenzene derivative and intermolecular hydrogen bonds have been measured in the temperature range from 30 to 200 degrees C to investigate heat-induced structural changes and thermal stability. Principal component analysis (PCA) and two kinds of two-dimensional (2D) correlation spectroscopy, variable-variable (VV) 2D and sample-sample (SS) 2D spectroscopy, have been employed to analyze the observed temperature-dependent spectral variations. The PCA and SS 2D correlation analyses have demonstrated that the complete decoupling of hydrogen bonds in the supramolecular assembly occurs between 110 and 115 degrees C, which is in good agreement with the results of a differential scanning calorimetry (DSC) study for the heating process. The PCA of the IR spectra in the region of 3600-3100 cm(-1) has illustrated that there are at least four principal components for the different NH2 and CONH species in the present supramolecular system. The VV 2D correlation spectroscopy study has provided information about the structure and strength of hydrogen bonds of NH2 and CONH groups and their temperature-dependent variations. The different species of hydrogen-bonded NH2 and CONH groups in the supramolecular system can be clarified by the VV 2D correlation analysis. The VV 2D correlation analysis has also revealed the specific order of the temperature-induced changes in the hydrogen bonds of NH2 and CONH groups.

Azo Compounds↗
PubMed2003

Temperature-dependent near-infrared spectra of bovine serum albumin in aqueous solutions: spectral analysis by principal component analysis and evolving factor analysis.

Fourier transform near-infrared (FT-NIR) spectra have been measured for bovine serum albumin (BSA) in an aqueous solution (pH 6.8) with a concentration of 5.0 wt% over a temperature range of 45-85 degrees C. Not only conventional spectral analysis methods, such as second-derivative spectra and difference spectra, but also chemometrics, such as principal component analysis (PCA) and evolving factor analysis (EFA), have been employed to analyze the temperature-dependent NIR spectra in the 7500-5500 and 4900-4200 cm-1 regions of the BSA aqueous solution. Intensity changes of bands in the 7200-6600 cm-1 and 4650-4500 cm-1 regions in the difference spectra indicate variations of the hydration and secondary structure of BSA in the aqueous solution, respectively. The plot of a band intensity at 7080 cm-1 in the different spectra shows a clear turning point at 63 degrees C, revealing that a significant change in the hydration occurs at about 63 degrees C. The forward and backward eigenvalues (EVs) from EFA suggest that marked changes in the hydration and secondary structure of BSA take place in the temperature ranges of 61-65 degrees C and 59-63 degrees C, respectively. In addition, the temperature of 71 degrees C marked in the EFA plots may correspond to the onset temperature of increase in the intermolecular beta-sheet structure.

Animals↗