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Xiang Ma

Publications and source records attributed to Xiang Ma.

At least 19 recordsLinked to original sources
PubMed2026

Functional Characterization of the Oat (Avena sativa L.) TCP Transcription Factor AsTCP38 Reveals Its Role in Low-Nitrogen Stress Tolerance.

Nitrogen limitation restricts plant growth, development, and yield in crops and forage species. Although TCP transcription factors are implicated in diverse abiotic-stress responses, the functions of most TCP genes in oat remain unclear. Here, we cloned and characterized the AsTCP38 gene, which is 1215 bp long and encodes a 405-amino-acid protein. The predicted protein contains a conserved TCP domain and shares its highest sequence similarity with Arabidopsis thaliana (A. thaliana) AtTCP15. The AsTCP38 protein localized to the nucleus, and promoter analysis identified cis-elements associated with light, hormone, and stress responses. We generated AsTCP38-overexpressing A. thaliana and wheat plants and screened an oat leaf yeast cDNA library for candidate interacting proteins. In these heterologous overexpression lines, AsTCP38 overexpression was associated with greater abscisic acid (ABA) sensitivity and improved seedling growth under low-nitrogen conditions. Changes in antioxidant-enzyme activities, nitrogen-metabolism-related enzyme activities, and endogenous hormone contents were also observed. Together, these findings suggest that AsTCP38 may participate in low-nitrogen responses and provide a basis for further functional studies in oat. Direct regulatory targets and the contribution of AsTCP38 to low-nitrogen adaptation in oat remain to be established.

Avena↗
PubMed2026

Exploring the mechanism of Acanthopanax in treating vertigo: A network pharmacology and molecular docking study.

Acanthopanax has therapeutic efficacy against vertigo; however, the underlying mechanism remains unclear. This study aimed to elucidate the mechanism by which Acanthopanax treats vertigo through integrated network pharmacology and molecular docking techniques, and retrieved all target genes of Acanthopanax for vertigo treatment from July to October 2025. Vertigo-related target genes were subsequently identified from public databases, including GeneCards and Online Mendelian Inheritance in Man. The intersection between Acanthopanax-derived targets and vertigo-related targets was analyzed to identify candidate target genes. Using the STRING platform, we constructed protein-protein interaction networks for the identified candidate targets and mined the core functional modules within these networks. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed on candidate targets via the clusterProfiler package. A carp bile poisoning-liver injury target-pathway network was constructed via Cytoscape 3.8.2 software, network topology analysis was conducted, and the core components and targets were screened. The results found that A total of 295 candidate targets for the treatment of vertigo caused by Eleutherococcus senticosus were identified. Pathway enrichment analysis revealed that Eleutherococcus senticosus treatment for vertigo may be closely associated with pathways related to IL-17, TNF, phosphoinositide 3-kinase (PI3K)-Akt, p53, HIF-1, and Forkhead box O signaling. The core targets for the treatment of A. senticosus vertigo include TP53, AKT1, STAT3, TNF, and JUN. Network pharmacology and molecular docking studies suggest that A. senticosus may treat vertigo by regulating targets such as JUN, TNF, AKT1, STAT3, and STAT3 through pathways such as the IL-17, TNF, phosphoinositide 3-kinase-Akt, p53, HIF-1, and Forkhead box O signaling pathways. These mechanisms warrant further investigation in future o and in vitro studies.

Molecular Docking Simulation↗
PubMed2026

How not to be seen: predicting unseen enzyme functions using contrastive learning.

MOTIVATION: Predicting enzyme function from its sequence is still an unsolved problem in the life sciences. Moreover, with the explosion of annotated genome data, we are inundated with potential enzymatic sequences that have not yet been biochemically characterized. While it is not possible to assign a not-yet-existing label to such a sequence, there is high value in placing the sequence as accurately as possible in known function space. Doing so can help provide more accurate falsifiable hypotheses for experimentalists wishing to characterize enzymes from specific functional families. RESULTS: Here we present a contrastive learning algorithm for predicting enzyme function from sequence. Our method, EnzPlacer, predicts the third, second, and first EC numbers for a protein whose fourth EC number is not in the training corpus. This novel prediction mechanism accurately places a protein sequence within a narrowed-down functional context, even if the precise function remains unknown. AVAILABILITY AND IMPLEMENTATION: EnzPlacer and data is available at https://github.com/drxiangma/EnzPlacer under a GPL3 license.

Enzymes↗
PubMed2026

How Not to be Seen: Predicting Unseen Enzyme Functions using Contrastive Learning.

MOTIVATION: Predicting enzyme function from its sequence is still an unsolved problem in the life sciences. Moreover, with the explosion of annotated genome data, we are inundated with potential enzymatic sequences that have not yet been biochemically characterized. While it is not possible to assign a not-yet-existing label to such a sequence, there is high value in placing the sequence as accurately as possible in known function space. Doing so can help provide more accurate falsifiable hypotheses for experimentalists wishing to characterize enzymes from specific functional families. RESULTS: Here we present a contrastive learning algorithm for predicting enzyme function from sequence. Our method, EnzPlacer, predicts the third, second, and first EC numbers for a protein whose fourth EC number is not in the training corpus. This novel prediction mechanism accurately places a protein sequence within a narrowed-down functional context, even if the precise function remains unknown. AVAILABILITY: EnzPlacer is available from https://github.com/drxiangma/EnzPlacer under a GPL3 license.

Contrastive learning↗
PubMed2006

[Prognostic value of E-cadherin, CD34 in the patients with hepatocellular carcinoma].

OBJECTIVE: To study the expression of E-cadherin and CD34 in the tissues of hepatocellular carcinoma (HCC), to discuss the relationship between them and the clinical pathology and evaluate the prognosis of HCC patients. METHODS: The expression of E-cadherin and CD34 in HCC tissues of 41 patients were examined by two-step methods of PV-6000 of immunohistochemistry. Clinical-pathological data, tumor recurrent rate and survival rate after hepatectomy were recorded and analyzed. RESULTS: The positive expression rate was observed in 48.78% for E-cadherin and 100% for CD34. The decreased E-cadherin expression were significantly associated with larger tumor, the high-dangerous group with invasion and poor differentiation of HCC tissues (chi(2) = 4.1881, 4.8118, 6.2695, P < 0.05). In the group with negative-expression of E-cadherin, the percent of tumor recurrence within 2 years after hepatectomy was higher and the rate of 5 years survival was significantly lower than the positive-expressed group. A significant negative-correlation between the expression of CD34 and the patients' age and the invasion of tumor (t = 1.9371, 1.9010, P < 0.05) were found. There was no relationship between the expression of E-cadherin and CD34 in HCC tissues. CONCLUSIONS: The patient with a negative-expression of E-cadherin in HCC tissues has a poor prognosis. No relationship between the expression of CD34 and tumor recurrence and patients' survival and no relationship between the expression of E-cadherin and CD34 was found.

Adult↗
PubMed2006

Rapid, large-scale synthesis and electrochemical behavior of faceted single-crystalline selenium nanotubes.

This article describes a rapid, solution-phase approach to the large-scale synthesis of faceted single-crystalline Se nanotubes, in the presence of cetyltrimethylammonium bromide. The products were characterized by scanning electron microscopy, high-resolution transmission electron microscopy, X-ray diffraction, X-ray photoelectron spectroscopy, laser Raman spectrography, differential scanning calorimetry analysis, and thermogravimetric analysis. The growth mechanism of the Se nanotubes was investigated by a series of experiments, and the rationality of the faceted morphology model for the Se nanotubes was demonstrated from the energetics and geometry. Furthermore, the electrochemical behavior of the Se nanotubes was studied by voltammetric techniques.

Calorimetry, Differential Scanning↗
PubMed2006

Unidirectional threading synthesis of isomer-free [2]rotaxanes.

The threading of an alpha-cyclodextrin (alpha-CyD) by an unsymmetrical dumbbell generally results in two isomeric [2]rotaxanes differing in the orientation of the alpha-CyD. In this work, two methods have been developed for the unidirectionally threading an alpha-CyD to obtain isomer-free [2]rotaxanes. These methods use the Suzuki coupling of a boronic acid derivative and a halide in aqueous alkaline solution. The conformations of the two unidirectional [2]rotaxanes-R3 and R4 were determined by 2D 1H ROESY NMR spectra. The optical spectral studies revealed that each of the two [2]rotaxanes can proceed with E/Z photoisomerization and shuttling motions of the alpha-CyD ring on the thread under alternating irradiation at 330 and 275 nm, accompanied by fluorescence intensity changes at 530 nm. The induced circular dichroism (ICD) spectra of another two analogous [2]rotaxanes R1 and R2 were also studied. Distinctive ICD signal changes resulting from the photoisomerization with respect to the movements of alpha-CyD were detected. This demonstrates that, besides the fluorescence, ICD signal is another way to identify the shuttling motions of alpha-CyD in these [2]rotaxanes.

Journal Article↗
PubMed2005

A [3]rotaxane with three stable states that responds to multiple-inputs and displays dual fluorescence addresses.

A [3]rotaxane molecular shuttle containing two alpha-cyclodextrin (alpha-CD) macrocycles, an azobenzene unit, a stilbene unit, and two different fluorescent naphthalimide units has been investigated. The azobenzene unit and the stilbene unit can be E/Z-photoisomerized separately by light excited at different wavelengths. Irradiation at 380 nm resulted in the photoisomerization of the azobenzene unit, leading to the formation of one stable state of the [3]rotaxane (Z1-NNAS-2CD); irradiation at 313 nm resulted in the photoisomerization of the stilbene unit, leading to the formation of another stable state of the [3]rotaxane (Z2-NNAS-2CD). The reversible conversion of the Z1 and Z2 isomers back to the E isomer by irradiation at 450 nm and 280 nm, respectively, is accompanied by recovery of the absorption and fluorescence spectra of the [3]rotaxane. The E isomer and the two Z isomers have been characterized by 1H NMR spectroscopy and by two-dimensional NMR spectroscopy. The light stimuli can induce shuttling motions of the two alpha-CD macrocycles on the molecular thread; concomitantly, the absorption and fluorescence spectra of the [3]rotaxane change in a regular way. When the alpha-CD macrocycle stays close to the fluorescent moiety, the fluorescence of the moiety become stronger due to the rigidity of the alpha-CD ring. As the photoisomerization processes are fully reversible, the photo-induced shuttling motions of the alpha-CD rings can be repeated, accompanied by dual reversible fluorescence signal outputs. The potential application of such light-induced mechanical motions at the molecular level could provide some insight into the workings of a molecular machine with entirely optical signals, and could provide a cheap, convenient interface for communication between micro- and macroworlds.

Journal Article↗
PubMed2005

A two-dimensional electrophoresis reference map of human ovary.

The ovary plays a central role in oogenesis and gonadal hormone secretion. Proteomic analysis is a valuable approach for gaining an increased understanding of the molecular nature of the ovary. In this work, two-dimensional electrophoresis for protein separation followed by matrix-assisted laser desorption/ionization mass spectrometry and database searches, identified 231 protein spots corresponding to 138 individual proteins that were found in gels representing both the follicular and luteal phases. The data were used to construct a database online (http://reprod.njmu.edu.cn/2d). The identified proteins were functionally classified into seven groups: (1) cell signaling/communication, (2) cell division, (3) gene/protein expression, (4) metabolism, (5) cell structure and motility, (6) cell/organism defense, and (7) unclassified. Among the proteins identified, 47% had not been previously reported in the human ovary. In addition, a number of disease-related proteins were identified in this protein map, including some cancer- and polycystic ovarian syndrome-related proteins. Two proteins with phosphorylation were verified by Western blot analysis. Comparison of protein abundance between follicular and luteal stages produced seven protein spots that had been identified in our database. This study provides a preliminary reference map of normal human ovary that will form a basis for comparative studies on normal and pathological conditions of the human ovary and may serve as a potential tool for clinical diagnosis, therapeutics, and prognosis.

Animals↗
PubMed2005

Direct electrochemistry and electrocatalysis of hemoglobin in poly-3-hydroxybutyrate membrane.

Hemoglobin (Hb) can take direct electron-transfer reactions after being entrapped in poly-3-hydroxybutyrate (PHB) film. A pair of well-defined, quasi-reversible cyclic voltammetric peaks is thus obtained at an Hb-PHB modified pyrolytic graphite electrode. The anodic and cathodic peaks are located at -224 and -284 mV for a pH 5.0 acetate buffer solution. Meanwhile, the peroxidase activity of the protein in the membrane has been greatly enhanced, with the apparent Michaelis-Menten constant calculated to be 1076 microM. According to the direct electron transfer property and enhanced peroxidase activity of Hb in the membrane, a Hb-PHB based hydrogen peroxide biosensor is prepared, with a linear range 6.0 x 10(-7) to 8.0 x 10(-4) M. The pathway of reductive dehalogenation of trichloroacetic acid is also discussed in detail. The highly reduced form of Hb produced in PHB film can be used to dechlorinate di- and monochloroacetic acid. The catalytic ability of Hb toward the reduction of nitric oxide has been investigated as well. Due to its biodegradability, low cost, chemical inertness, and especially its biocompatibility and non-toxicity, PHB would be a desirable film in the sensor field.

Biosensing Techniques↗
PubMed2005

Electrochemical studies on polysorbate-20 (Tween 20)-entrapped haemoglobin and its application in a hydrogen peroxide biosensor.

Haemoglobin (Hb) was entrapped in polysorbate 20 and then modified on a pyrolytic graphite electrode. Electrochemical studies revealed that a pair of stable and well-defined redox peaks attributed to the direct redox reaction of Hb could be observed in a phosphate buffer solution (pH 6.0). The anodic and cathodic peaks were located at -236 and -316 mV (versus a saturated calomel reference electrode) separately. The formal potential, E0', was linearly varied with pH in the range from 3.0 to 10.0 with a slope of -48.0 mV.pH-1. Moreover, the protein was capable of catalysing the reduction of H2O2. Accordingly, an unmediated biosensor for H2O2 was prepared with a linear range from 8.0x10(-7) to 1.0x10(-3) M. This biosensor exhibited good stability, sensitivity and reproducibility.

Biosensing Techniques↗
PubMed2005

Anti-SARS-CoV immunoglobulin G in healthcare workers, Guangzhou, China.

To determine the prevalence of inapparent infection with severe acute respiratory syndrome (SARS) among healthcare workers, we performed a serosurvey to test for immunoglobulin (Ig) G antibodies to the SARS coronavirus (SARS-CoV) among 1,147 healthcare workers in 3 hospitals that admitted SARS patients in mid-May 2003. Among them were 90 healthcare workers with SARS. As a reference group, 709 healthcare workers who worked in 2 hospitals that never admitted any SARS patients were similarly tested. The seroprevalence rate was 88.9% (80/90) for healthcare workers with SARS and 1.4% (15/1,057) for healthcare workers who were apparently healthy. The seroprevalence in the reference group was 0.4% (3/709). These findings suggest that inapparent infection is uncommon. Low level of immunity among unaffected healthcare workers reinforces the need for adequate personal protection and other infection control measures in hospitals to prevent future epidemics.

Adult↗
PubMed2005

Corneal neovascularization suppressed by TIMP2 released from human amniotic membranes.

PURPOSE: To investigate the effects of culture medium of human amniotic membrane (AM) on corneal neovascularization (CNV) induced by basic fibroblast growth factor (bFGF) in mice. METHODS: Culture medium of amniotic membrane was prepared by cultivating AM (with epithelium side up) in EGM basic medium for 3 days, and was collected separately to three groups, e.g. control (EGM only), AM with epithelium (AM) and AM without epithelium (De-AM). Corneal neovascularization was induced in mice by using micropocket assay with Hydron polymer pellets containing 100 ng bFGF. Migration and proliferation of human umbilical cord vein endothelial cells (HUVEC) were performed in Boyden chambers and by using the CyQUANT fluorescence binding assay respectively. The levels of tissue inhibitors of metalloproteinase 1 and 2 (TIMP1, TIMP2) in culture medium were determined by ELISA assay. RESULTS: CNV induced by bFGF was significantly suppressed by culture medium of amniotic membrane. When the medium was applied as an eyedrop 4 times a day for 7 days, the area of CNV was (2.48+/-0.76) mm(2),(0.64+/-0.52) mm(2) and (1.96+/-0.65) mm(2) in control, AM and De-AM group respectively. The migration and proliferation of HUVEC were strongly inhibited by culture medium of AM with epithelium, while the De-AM had no effect on the migration of HUVEC cells. The high level of TIMP2 was found in AM group, but not in De-AM group, while there was no difference in the amount of TIMP1 in medium among three groups. CONCLUSION: Culture medium of amniotic membrane significantly suppresses the corneal nevovascularization induced by bFGF. The mechanism of which at least in part is that high level of TIMP2 protein secreted or released into the culture medium of AM and inhibition of migration and growth of vascular endothelial cells.

Amnion↗
PubMed2004

Differential expression of glucose-regulated protein 78 during spermatogenesis.

The aim of the present study was to isolate and identify proteins involved in the process of spermatogenesis. To achieve this goal we used the technique of proteomic analysis. Comparison of testis protein patterns obtained by high-resolution two-dimensional gel electrophoresis from 1-week- and 7-week-old mice showed significant differences in protein spot intensities. Subsequently several of these variant protein spots were identified by mass spectrometry. Glucose-regulated protein (GRP) 78 (Bip) was one of them. GRP78, expressed at a lower level in 1-week-old mouse testes compared to 7-week-old mouse testes, is a member of the heat shock 70 protein family. It has recently been shown to be important for protecting cells from apoptosis in somatic cells, especially in progressively growing tumor cells. Further, immunohistochemical (IHC) analyses of mouse and human testes sections were performed to determine the cellular distribution of this protein. A strong GRP78 staining was seen beginning with pachytene spermatocytes. These findings suggested that GRP78 might perform an important function in the process of spermatogenesis.

Age Factors↗
PubMed2004

Platelet-activating factor (PAF) induces corneal neovascularization and upregulates VEGF expression in endothelial cells.

PURPOSE: Platelet-activating factor (PAF) is a potent proinflammatory mediator that accumulates in the cornea after injury and induces the expression of genes related to inflammation and wound healing. The current study was conducted to investigate the direct effect of PAF on corneal neovascularization and on the expression of angiogenic growth factors in vascular endothelial cells. METHODS: Pellets containing carbamyl-PAF (cPAF) were implanted in corneas of wild-type or PAF-receptor (PAF-R)-knockout mice, and the progression of angiogenesis was monitored by microscope. In some experiments, mice were treated with a daily intraperitoneal injection of the PAF-R antagonist LAU8080. Migration assays of human umbilical cord vein endothelial cells (HUVECs) and human dermal microvascular endothelial cells (HMVECs) were performed in a Boyden chamber after addition of various concentrations of cPAF or bovine fibroblast growth factor (FGF-2). Cell proliferation was assessed by fluorescence-binding assay in the presence of cPAF or FGF-2 for 8 days. Vascular endothelial growth factor (VEGF) and FGF-2 expression was studied by RT-PCR and Northern- and Western-blot analyses in cells stimulated with cPAF at different concentrations and for different times. RESULTS: Six days after cPAF pellet implantation, there were new vessels growing from the limbus to the center of the cornea. The PAF-induced neovascularization was significantly reduced in PAF-R-knockout mice and in mice treated with the PAF antagonist. cPAF added to the lower well of the Boyden chamber produced a dose-dependent migration of HUVECs and HMVECs that was inhibited in cells preincubated with LAU8080 or with a VEGF-blocking antibody. In contrast, cPAF did not stimulate proliferation of endothelial cells. cPAF induced VEGF mRNA and protein expression but not FGF-2 expression in HUVECs and HMVECs. CONCLUSIONS: PAF stimulates corneal neovascularization by a receptor-mediated mechanism. Induction of VEGF expression and stimulation of vascular endothelial cell migration are initial events in PAF-promoted corneal angiogenesis.

Animals↗
PubMed2004

[Corneal epithelial wound healing is delayed by platelet activating factor treatment].

OBJECTIVE: To investigate the role of PAF in corneal epithelial wound healing and its mechanisms. METHODS: Rabbit corneal epithelial (RCE) and keratocyte (RCK) cells were cultured and used at passage 2 to 3. For the in vitro wound healing experiments, a 7 mm central corneal de-epithelialization was performed in rabbit corneas. Corneas were incubated in the presence of 100 nmol/L PAF; 4 micro mol/L of the PAF antagonist BN was added 30 min before PAF. The area of the cornea uncovered by the epithelium was measured after 48 h using an imaging system. Cell adhesion, proliferation and migration were analyzed using CyQUANT fluorescence binding assay and Boyden chamber respectively. RNA was extracted and RT-PCR and Northern blot analyses were performed using HGF, KGF, EGF and HGF-R primers and probes. RESULTS: Forty-eight hours after the wound, the uncovered area (in arbitrary units) for control corneas was (6.0 +/- 1.5) U. PAF dramatically inhibited corneal epithelial wound closure, and the uncovered area was (58.0 +/- 7.0) U. The PAF antagonist completely abolished the effect of PAF with values similar to controls (5.0 +/- 1.0) U. PAF significantly increased the cell adhesion among RCE cells, while at the concentration of 100 nmol/L, PAF had no effect on the proliferation and migration of RCE cells. RT-PCR results revealed that PAF at 100 nmol/L decreased the HGF mRNA expression 4.1 times in RCK and HGF-R 3.5 times in RCE at 24 h compared to control group, while PAF had no effect on the expression of KGF and EGF in RCE cells. Northern blot data confirmed these results. CONCLUSIONS: Our results suggest that PAF causes significant delay of corneal epithelial wound healing. This effect may partially be due to the increased RCE cell adhesion and suppressed expression of HGF gene in RCK and HGF-R. The PAF antagonist BN can completely abolish the effect of PAF and enhance the corneal wound repair.

Animals↗
PubMed2004

[A two-dimensional reference map of mouse ovary proteins].

OBJECTIVE: To perform a preliminary proteomic analysis of mouse ovaries and to study the protein's function in mouse ovary. METHODS: The two-dimensional gel electrophoresis (2-DE) and matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) were used to analyze mouse ovarian proteome. A 12.5% sodium dodecyl sulfate (SDS) reference gel was generated by immobilized pH gradient isoelectric focusing of mouse ovary proteins in a non-linear gradient (pH 3-10). And GRP78 was selected to perform with immunohistochemistry within mouse ovaries. RESULTS: Based on peptide mass fingerprinting, 52 proteins were identified and classified into seven functional groups: Cell/organism defense and antioxidant, cell signaling/communications proteins, cell structure/motility proteins, metabolism proteins, RNA synthesis processing, protein synthesis and processing, and unclassified proteins. The immunoreactivity of GRP78 was detected in GCs in the follicular, and with during GCs Luteinizing in the menstrual cycle, the protein expression (brown) increased continually and came to a head when ovulation happened. CONCLUSION: This work provides a first step toward the establishment of a systematic ovary protein database and stands as a valuable resource for molecular analyses of normal and pathologic conditions affecting mouse ovaries.

Animals↗