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Xiaoyu Yang

Publications and source records attributed to Xiaoyu Yang.

At least 19 recordsLinked to original sources
PubMed2026

Genome-Wide Characterization and Salt-Responsive Expression Divergence of Chromosome Group 2 and Group 6 TaBADH Genes in Wheat.

Betaine aldehyde dehydrogenase (BADH) catalyzes the final step in glycine betaine biosynthesis, but the evolutionary divergence and differential salt responsiveness of BADH homeologs in bread wheat remain unclear. We identified six TaBADH genes and analyzed their phylogenetic relationships, conserved motifs, gene structures, promoter cis-acting elements and synteny. RNA-seq and qRT-PCR were used to compare expression in salt-tolerant Jimai 60 and salt-sensitive Chinese Spring under 200 mM NaCl, and BADH activity, glycine betaine, H2O2 and malondialdehyde (MDA) were measured during treatment. The genes separated into chromosome group 2 and group 6 clades with distinct structural and transcriptional patterns. TaBADH-2B encoded a shorter protein and lacked several conserved motifs. Group 6 genes showed stronger salt-responsive expression in Jimai 60, with TaBADH-6D displaying the strongest and most sustained induction. Jimai 60 also showed higher BADH activity and glycine betaine accumulation and lower H2O2 and MDA contents at later time points. Expression of TaBADH-6D improved E. coli growth under 200 mM NaCl. These findings identify homeolog-specific divergence within the BADH wheat family and support TaBADH-6D as a candidate for plant-level functional validation.

TaBADH-6D↗
PubMed2026

Host-driven evolution shapes the polysaccharide utilization profiles of alga-associated Flavobacteriaceae.

BACKGROUND: Marine algae represent major producers of complex polysaccharides and serve as hosts for diverse microbial communities in the phycosphere. Flavobacteriaceae are among the key bacterial taxa involved in polysaccharide degradation and carbon remineralization in this environment. However, the extent to which algal hosts drive the divergence of polysaccharide utilization profiles in these bacteria remains unclear. RESULTS: We conducted a genome-resolved analysis of 103 cultured Flavobacteriaceae strains isolated from red, green, and brown macroalgae, as well as from diatoms and dinoflagellates. We found that macroalga-associated strains generally harbored more abundant and diverse CAZyme-encoding genes than their microalga-associated counterparts. Moreover, strains associated with different algal phyla showed distinct metabolic specializations that aligned with the typical polysaccharides of their respective hosts, strongly supporting host-specific adaptation. In four widely distributed genera (Maribacter, Flagellimonas, Polaribacter, Winogradskyella), CAZyme profile dissimilarity and key glycoside hydrolase gene divergence exhibited phylogenetic congruence with algal host phylogeny (Mantel r up to 0.76 and 0.85, respectively), indicative of host-associated functional adaptation. Using Maribacter as a model, cultivation experiments and transcriptome characterization demonstrated that polysaccharide utilization efficiency is not solely linked to the organization of genes into polysaccharide utilization loci (PULs), but also associated with the expression dynamics of key transcription factors (TFs), particularly those from AraC and DeoR families, whose expression patterns were coordinated with laminarin degradation. Notably, these two TF families also exhibited host-associated divergence patterns similar to those of CAZyme-encoding genes. Furthermore, analysis of the Tara Oceans metagenomic data indicated that, within the AraC and DeoR families, a higher proportion of genes were positively correlated with chlorophyll a content compared to other TF families, reinforcing their specialized roles in alga-associated bacterial lifestyles. CONCLUSIONS: Our integrative genomic and transcriptomic analyses reveal evolutionary and regulatory adaptation of marine Flavobacteriaceae to distinct algal hosts. These findings highlight algae-derived habitats as specialized niches that shape microbial metabolic potential, and suggest that carbohydrate metabolism plays a key role in host-driven bacterial evolution across global oceans. Video Abstract.

Flavobacteriaceae↗
PubMed2006

Dehydration versus deamination of N-terminal glutamine in collision-induced dissociation of protonated peptides.

Some of the most prominent "neutral losses" in peptide ion fragmentation are the loss of ammonia and water from N-terminal glutamine. These processes are studied by electrospray ionization mass spectrometry in singly- and doubly-protonated peptide ions undergoing collision-induced dissociation in a triple quadrupole and in an ion trap instrument. For this study, four sets of peptides were synthesized: (1) QLLLPLLLK and similar peptides with K replaced by R, H, or L, and Q replaced by a number of amino acids, (2) QLnK (n = 0, 1, 3, 5, 7, 9, 11), (3) QLnR (n = 0, 1, 3, 5, 7, 9), and (4) QLn (n = 1, 2, 3, 4, 8). The results for QLLLPLLLK and QLLLPLLLR show that the singly protonated ions undergo loss of ammonia and to a smaller extent loss of water, whereas the doubly protonated ions undergo predominant loss of water. The fast fragmentation next to P (forming the y5 ion) occurs to a larger extent than the neutral losses from the singly protonated ions but much less than the water loss from the doubly protonated ions. The results from these and other peptides show that, in general, when N-terminal glutamine peptides have no "mobile protons", that is, the number of charges on the peptide is no greater than the number of basic amino acids (K, R, H), deamination is the predominant neutral loss fragmentation, but when mobile protons are present the predominant process is the loss of water. Both of these processes are faster than backbone fragmentation at the proline. These results are rationalized on the basis of resonance stabilization of the two types of five-membered ring products that would be formed in the neutral loss processes; the singly protonated ion yields the more stable neutral pyrrolidinone ring whereas the doubly protonated ion yields the protonated aminopyrroline ring (see Schemes). The generality of these trends is confirmed by analyzing an MS/MS spectra library of peptides derived from tryptic digests of yeast. In the absence of mobile protons, glutamine deamination is the most rapid neutral loss process. For peptides with mobile protons, dehydration from glutamine is far more rapid than from any other amino acid. Most strikingly, end terminal glutamine is by far the most labile source of neutral loss in excess-proton peptides, but not highly exceptional when mobile protons are not available. In addition, rates of deamination are faster in lysine versus arginine C-terminus peptides and 20 times faster in positively charged than negatively charged peptides, demonstrating that these formal neutral loss reactions are not "neutral reactions" but depend on charge state and stability.

Amino Acid Sequence↗
PubMed2006

Adolescent lumbar disc herniation and hamstring tightness: review of 16 cases.

STUDY DESIGN: Retrospective review. OBJECTIVES: To investigate the clinical characteristics and responses to surgical and conservative treatments of lumbar disc herniation in adolescents with hamstring tightness. SUMMARY OF BACKGROUND DATA: The incidence of hamstring tightness in adolescent lumbar disc herniation is much higher than that of adults. Hamstring tightness has been reported to result from nerve root or cauda equina irritation. But the clinical characteristics, prognosis, and etiologic mechanism of hamstring tightness has not been clearly investigated. METHODS: Sixteen consecutive adolescents (age range, 12-18 years; mean, 15.8 years) with lumbar disc herniation were analyzed. Among them, there were 10 cases with hamstring tightness. Clinical and radiologic findings of the study group were compared with those of the remaining 6 cases. After conservative treatment, 5 cases in the hamstring tightness group were treated with discectomy, and of these, 1 case was treated with shortening osteotomy in the upper part of the bilateral femurs 10 months after the discectomy because of the persisting hamstring tightness. Another 5 discectomies were done in the nonhamstring tightness group. All patients were observed for a mean of 2.7 years (range, 0.8-6 years). RESULTS: In all patients, the neurologic defects were improved shortly after the treatment, but the hamstring tightness continued and remained even after 1 year. The patient who underwent femoral osteotomy showed improvement. CONCLUSIONS: The incidence of hamstring tightness in adolescent lumbar disc herniation is high. The physical examination findings and prognoses of patients with hamstring tightness are different from those of simple disc herniation patients. The hamstring tightness appeared to have developed from a different mechanism.

Adolescent↗
PubMed2006

Micromolding of photocrosslinkable chitosan hydrogel for spheroid microarray and co-cultures.

Bioengineering approaches, such as co-cultures of multiple cell types, that aim to mimic the physiological microenvironment may be beneficial for optimizing cell function and for engineering tissues in vitro. This study describes a novel method for preparing a spheroid microarray on microfabricated hydrogels, alone or in co-cultures. Photocrosslinkable chitosan was synthesized and utilized for fabricating hydrogel microstructures through a micromolding process. The chitosan surface was initially cell repellent but became increasingly cell adhesive over time. By using this unique property of chitosan hydrogels, it was possible to generate patterned co-cultures of spheroids and support cells. In this scheme, cells were initially microarrayed within low shear stress regions of microwells. Human hepatoblastoma cells, Hep G2, seeded in these wells formed spheroids with controlled sizes and shapes and stably secreted albumin during the culture period. The change of cell adhesive properties in the chitosan surface facilitated the adhesion and growth of a second cell type, NIH-3T3 fibroblast, and therefore enabled co-cultures of hepatocyte spheroids and fibroblast monolayers. This co-culture system could be a useful platform for studying heterotypic cell-cell interactions, for drug screening, and for developing implantable bioartificial organs.

Animals↗
PubMed2006

Dynamic canal encroachment of ligamentum flavum: an in vitro study of cadaveric specimens.

OBJECTIVE: In extension of the cervical spine, the ligamentum flavum (LF) may bulge and intrude into the vertebral canal and cause symptoms of myelopathy and/or radiculopathy in patients with canal stenosis. Knowledge of the relationship between the extension angle and the physiologic changes of the LF is important for a better understanding of the clinical symptoms. The current study was designed to demonstrate the dynamic correlativity of canal intrusion of the LF bulge with the extension angle of the cervical spine. METHODS: With a novel method, the probe of the electrical resistance strain gauge was put into the cervical canals of 14 cadaveric specimens. The LF bulge distance of six segments (C2-C3 to C7-T1) and corresponding extension angles of every 5 degrees from 0 degrees to 45 degrees were collected. Angle-bulge curves were drawn. RESULTS: In overextension (45 degrees ), C5-C6 had the biggest canal intrusion depth (3.478+/-0.527 mm), whereas the upper and lower segments declined gradually (C5-C6>C4-C5>C6-C7>C3-C4>C7-T1>C2-C3). The curves in all segments were sigmoidal, which demonstrated the dynamic change of LF, that is, during the process of extension, LF shortened and contracted first, after the original length was reached, it began to bulge and burst into the canal. CONCLUSION: The current study has provided a method to measure inner canal kinematic changes in intact spinal specimens.

Adult↗
PubMed2005

A layered goal-oriented fuzzy motion planning strategy for mobile robot navigation.

Most conventional motion planning algorithms that are based on the model of the environment cannot perform well when dealing with the navigation problem for real-world mobile robots where the environment is unknown and can change dynamically. In this paper, a layered goal-oriented motion planning strategy using fuzzy logic is developed for a mobile robot navigating in an unknown environment. The information about the global goal and the long-range sensory data are used by the first layer of the planner to produce an intermediate goal, referred to as the way-point, that gives a favorable direction in terms of seeking the goal within the detected area. The second layer of the planner takes this way-point as a subgoal and, using short-range sensory data, guides the robot to reach the subgoal while avoiding collisions. The resulting path, connecting an initial point to a goal position, is similar to the path produced by the visibility graph motion planning method, but in this approach there is no assumption about the environment. Due to its simplicity and capability for real-time implementation, fuzzy logic has been used for the proposed motion planning strategy. The resulting navigation system is implemented on a real mobile robot, Koala, and tested in various environments. Experimental results are presented which demonstrate the effectiveness of the proposed fuzzy navigation system.

Algorithms↗
PubMed2004

Characterizing complex peptide mixtures using a multi-dimensional liquid chromatography-mass spectrometry system: Saccharomyces cerevisiae as a model system.

A rugged, reproducible, multi-dimensional LC-MS system was developed to identify and characterize proteins involved in protein-protein interactions and/or protein complexes. Our objective was to optimize chromatographic parameters for complex protein mixture analyses using automated peptide sequence recognition as an analytical end-point. The chromatographic system uses orthogonal separation mechanisms by employing strong cation exchange (SCX) in the first dimension and reversed phase (RP) in the second dimension. The system is fully automated and sufficiently robust to handle direct injections of protein digests. This system incorporates a streamlined post analysis results comparison, called DBParser, which permitted comprehensive evaluation of sample loading and chromatographic conditions to optimize the performance and reproducibility. Peptides obtained from trypsin digestion of a yeast soluble extract provided an open-ended model system containing a wide variety and dynamic range of components. Conditions are described that resulted in an average (n = 4) of 1489 unique peptide identifications, corresponding to 459 non-redundant protein sequence database records (SDRs) in the 20 microg soluble fraction digest.

Chromatography, Liquid↗
PubMed2004

Ordered mesoporous titanosilicates with catalytically stable and active four-coordinated titanium sites.

The stable ordered mesoporous titanosilicate (Ti-JLU-20) has been successfully synthesized from an assembly of mixed surfactants (fluorocarbon and triblock copolymer surfactants) with preformed titanosilicate zeolite precursors at high temperature (180-220 degrees C), and catalytic tests show that Ti-JLU-20 has highly stable and active four-coordinated titanium sites in oxidations.

Journal Article↗
PubMed2004

NMR experiments on a three-dimensional vibrofluidized granular medium.

A three-dimensional granular system fluidized by vertical container vibrations was studied using pulsed field gradient NMR coupled with one-dimensional magnetic resonance imaging. The system consisted of mustard seeds vibrated vertically at 50 Hz, and the number of layers N(l)<or=4 was sufficiently low to achieve a nearly time-independent granular fluid. Using NMR, the vertical profiles of density and granular temperature were directly measured, along with the distributions of vertical and horizontal grain velocities. The velocity distributions showed modest deviations from Maxwell-Boltzmann statistics, except for the vertical velocity distribution near the sample bottom, which was highly skewed and non-Gaussian. Data taken for three values of N(l) and two dimensionless accelerations Gamma=15,18 were fitted to a hydrodynamic theory, which successfully models the density and temperature profiles away from the vibrating container bottom. A temperature inversion near the free upper surface is observed, in agreement with predictions based on the hydrodynamic parameter micro which is nonzero only in inelastic systems.

Journal Article↗
PubMed2004

[Investigation of machinable-infiltrated-ceramic glass infiltrating through the aluminous matrix].

This investigation was amied at the infiltrative capability of the machinable-infiltrated-ceramic(MIC) glass and the color of the composite after the MIC glass infiltrated through the aluminous matrix with different packing densities. By heating the components to 1100 degrees C for 2 hours, the MIC glass was made to infiltrate through the aluminous matrix with different packing densities. We measured the infiltrative depth and the color parameter and observed the rupture surface of the composite by means of SEM. There was a linear relation between the square of infiltrative depth and the packing density of aluminous matrix. The minimal depth was 3.092 mm. No relationship was noted between the composite's color coefficient and the packing density of aluminous matrix. In the rupture process of the composite, crack deflexion, crystal evulsion, and rupture through crystal could be observed. This experiment proved that the infiltrative characters of MIC glass meet the clinical requirement, the composite's color is steady and the mechanical intensity is stable.

Aluminum Oxide↗
PubMed2003

[Study on infiltration glass for machinable-infiltrated-ceramic and on its colorants].

In order to develop tinted infiltration glass and its colorants, which can make the ceramic have good spectrum transmittance, color space, color stability and be suitable for clinical use, we selected the best prescription and confirm the ingredient and content of the colorants. Molten glass was prepared in Al2O3 crucible by heating the components to 1420 degrees C for 2 hours. The refractive index and thermal stability of the glass were investigated. The refractive index of the MIC infiltration glass was 1.5969(587.6 nm, nd). It was close to the index of aluminous matrix 1.759(546.07 nm, ne), which increased the spectrum transmittance of MIC. The thermal expansion coefficient of the glass was 7.565 microns/m/degree C, which was compatible with the thermal expansion coefficient of aluminous matrix(8.214 microns/m/degree C). This study proved that the tinted infiltration glass has good color stability, spectrum transmittance, and thermal expansion properties.

Aluminum Silicates↗
PubMed2002

Functional neutralization of HIV-1 Vif protein by intracellular immunization inhibits reverse transcription and viral replication.

Human immunodeficiency virus type 1 (HIV-1)-encoded Vif protein is important for viral replication and infectivity. Vif is a cytoplasmic protein that acts during virus assembly by an unknown mechanism, enhancing viral infectivity. The action of Vif in producer cells is essential for the completion of proviral DNA synthesis following virus entry. Therefore, Vif is considered to be an important alternative therapeutic target for inhibition of viral infectivity at the level of viral assembly and reverse transcription. To gain insight into this process, we developed a Vif-specific single-chain antibody and expressed it intracellularly in the cytoplasm. This intrabody efficiently bound Vif protein and neutralized its infectivity-enhancing function. Intrabody-expressing cells were shown to be highly refractory to challenge with different strains of HIV-1 and HIV-1-infected cells. Inhibition of Vif by intrabody expression in the donor cell produced viral particles that do not complete reverse transcription in the recipient cell. The anti-Vif scFv was shown to be specific for Vif protein because its function was observed only in nonpermissive cells (H9, CEM, and U38). Moreover, transduction of peripheral blood mononuclear cells with an HIV-derived retroviral vector expressing Vif intrabody was shown to confer resistance to laboratory-adapted and primary HIV strains. This study provides biochemical evidence for the role of Vif in the HIV-1 lifecycle and validates Vif as a target for the control of HIV-1 infection.

Animals↗
PubMed2002

Measurements of grain motion in a dense, three-dimensional granular fluid.

We have used an NMR technique to measure the short-time, three-dimensional displacement of grains in a system of mustard seeds vibrated vertically at 15 g. The technique averages over a time interval in which the grains move ballistically, giving a direct measurement of the granular temperature profile. The dense, lower portion of the sample is well described by a recent hydrodynamic theory for inelastic hard spheres. Near the free upper surface the mean free path is longer than the particle diameter and the hydrodynamic description fails.

Journal Article↗
PubMedDate not supplied

DBParser: web-based software for shotgun proteomic data analyses.

We describe a web-based program called 'DBParser' for rapidly culling, merging, and comparing sequence search engine results from multiple LC-MS/MS peptide analyses. DBParser employs the principle of parsimony to consolidate redundant protein assignments and derive the most concise set of proteins consistent with all of the assigned peptide sequences observed in an experiment or series of experiments. The resulting reports summarize peptide and protein identifications from multidimensional experiments that may contain a single data set or combine data from a group of data sets, all related to a single analytical sample. Additionally, the results of multiple experiments, each of which may contain several data sets, can be compared in reports that identify features that are common or different. DBParser actively links to the primary mass spectral data and to public online databases such as NCBI, GO, and Swiss-Prot in order to structure contextually specific reports for biologists and biochemists.

Amino Acid Sequence↗