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Xiaofeng Wang

Publications and source records attributed to Xiaofeng Wang.

At least 19 recordsLinked to original sources
PubMed2026

Dual Roles of RAD23b and RAD4 on the Desiccation Tolerance of Germinated Seeds.

Desiccation tolerance (DT) is a survival trait enabling orthodox seeds to withstand extremely low water content. While some protective factors are characterised, it remains mechanistically obscure. Here, based on PEG-induced DT re-establishment in germinated Brassica napus L. seeds, we investigated the dual functions of nucleotide excision repair (NER) components RAD23b and RAD4 in DNA repair and transcriptional regulation of root development. PEG pre-treatment alleviated dehydration-induced DNA damage and activated NER genes, suggesting the involvement of NER in seed DT. Unexpectedly, Arabidopsis atrad23b mutant and BnRAD23b/BnRAD4 over-expressing seeds all exhibited significantly decreased DT after dry back, which evoked a hypothesis that BnRAD23b-BnRAD4 functions beyond NER. Normally, BnRAD4 interacted with BnRAD23b and repressed the expression of root development genes NAC103, EMB1444, RRA1 by directly binding to STRE elements within their promoters. Dehydration stress alleviated this repression, drove transcriptional reprogramming and might redirect the complex to execute DNA repair. Genetic analyses revealed that germinated seeds of atnac103, atemb1444, and atrra1 single mutants all exhibited reduced DT, and double mutants under atrad23b background almost abolished DT. This study suggests that RAD23b and RAD4 may regulate DT re-establishment of germinated seeds through balancing genome integrity and radicle development, with implications for DT study broadly.

Brassica napus L.↗
PubMed2026

Feasibility of Prone Positioning in Patients With Obesity and Acute Respiratory Distress Syndrome.

BACKGROUND: Prone positioning in patients with obesity remains uncommon because of concerns about feasibility, safety, and efficacy. OBJECTIVE: To evaluate the feasibility, safety, and clinical outcomes of manual prone positioning in patients with acute respiratory distress syndrome (ARDS) across different classes of obesity. METHODS: This was a retrospective cohort study involving patients with ARDS who underwent manual prone positioning across 15 hospitals between April 2014 and July 2024. Patients were stratified into 5 groups based on body mass index. Standardized prone positioning protocols were followed across institutions. RESULTS: A total of 1448 patients with ARDS underwent prone positioning. Across all obesity categories, prone positioning was associated with shorter intensive care unit and hospital stays, improved oxygenation, and better clinical outcomes. Notably, patients with class III obesity showed the greatest increase in gas exchange efficiency, with a 37% improvement in ratio of Pao2 to fraction of inspired oxygen, compared with 28% in patients with normal weight (P < .05). Complication rates were low across all groups. CONCLUSIONS: Prone positioning is feasible and safe in patients with ARDS across all obesity classes. Patients with class III obesity showed the greatest improvements in oxygenation. Future prospective studies should further explore the long-term impact of prone positioning in patients with class III obesity to refine clinical guidelines and optimize care.

Humans↗
PubMed2026

Towards efficient perturbation for the noncoding genome.

Deciphering the functionality of the noncoding genome, which includes important cis-regulatory elements (CREs) and transcribed noncoding RNA genes, remains technically challenging. Here, using massively parallel genetic screening, we systematically benchmark the performance of five representative loss-of-function perturbation tools, including single-guide RNA (gRNA) mediated SpCas9 cleavage or CRISPR interference, and paired gRNA (pgRNA) involved dual-SpCas9, Big Papi (paired SpCas9 and SaCas9) or dual-enAsCas12a fragment deletion methods, in decoding the roles of the noncoding genome. For targeting CREs such as enhancers, dual-SpCas9 outperforms other methods with superior efficiency in destroying functional genomic regions. For perturbing noncoding RNA genes, in addition to dual-SpCas9, other RNA-targeting methods such as RNA interference are recommended to discriminate transcript-dependent or -independent roles. A deep learning model, DeepDC, with an associated web server, is built to facilitate optimal dual-SpCas9 pgRNA design for efficiently deleting a genomic fragment. Together, our work provides practical guidance on selecting appropriate loss-of-function tools to resolve the functional complexity of the noncoding genome.

CRISPR-Cas Systems↗
PubMed2025

Seq2Saccharide: Discovering Oligosaccharides and Aminoglycosides Natural Products by Integrating Computational Mass Spectrometry and Genome Mining.

Natural oligosaccharides and aminoglycosides are important sources of new drug candidates, especially in the development of antibiotics. In the past, discovering novel saccharides has been time-consuming and costly. However, the rapid expansion of high-throughput data, including genomic and mass spectrometry data sets, has greatly increased opportunities for natural saccharide discovery. Yet, due to the complex biosynthesis pathways of saccharides, no existing method can predict their structures with high precision. To address this, we introduce Seq2Saccharide, a tool designed to automate saccharide natural product discovery by integrating both genomic and mass spectrometry data. To enhance accuracy, Seq2Saccharide predicts hundreds or thousands of putative structures for each gene cluster. The correct structure is then identified from these predictions using a mass spectral search. Benchmarks against saccharides in the MiBIG database show that Seq2Saccharide outperforms existing methods in predicting the structure of saccharides. Furthermore, mass spectrometry analysis indicates that the variable search module can correct mispredictions from genome mining. By searching genomic and mass spectrometry data of microbial strains, Seq2Saccharide correctly identified the biosynthetic gene cluster for the polysaccharide oligosaccharide trestatin B.

Aminoglycosides↗
PubMed2025

Gut metagenome and plasma metabolome profiles in older adults suggest pyruvate metabolism as a link between sleep quality and frailty.

Poor sleep quality is associated with increased frailty in older adults, but the role of the gut microbiome in this relationship remains unclear. Here, gut metagenome and plasma metabolome were profiled in 1,225 individuals aged 62-96 years. Poor sleep quality was associated with reduced abundances of potential probiotics such as Faecalibacterium prausnitzii and elevated abundances of pathobionts. A gut microbiome sleep quality index (GMSI) was developed to quantify microbial balance related to better sleep quality; higher GMSI scores were inversely associated with frailty and related clinical traits. Pyruvate metabolism emerged as a key microbial pathway linking sleep quality to frailty, with features such as F. prausnitzii abundance and microbial pyridoxal 5'-phosphate biosynthesis implicated in this connection. These findings deepen our understanding of microbiome-metabolome pathways related to sleep quality and frailty in aging and provide a valuable resource for future longitudinal and interventional studies.

Humans↗
PubMed2006

Apoptotic related biochemical changes in human amnion cells induced by tributyltin.

Tributyltin (TBT) is one of the environmental pollutants, which is mostly accumulated in marine animals. The toxic effects of TBT have been extensively documented in several types of cells, but the molecular mechanisms responsible for TBT-induced cell damage are still not fully elucidated. The present study was undertaken to evaluate the apoptotic related biochemical changes in human amnion cells induced by TBT. After cells were exposed to TBT at the concentrations of 1-4 microM for 2h, the results suggested that TBT could induce an early and typical apoptosis, moreover caspase-3, the modifications of cytoskeletal structure and the Bcl-2 family were involved in this process. The results will deepen our understanding about the toxic mechanism of TBT on human amnion cells.

Amnion↗
PubMed2006

Quantifying degeneration of white matter in normal aging using fractal dimension.

Although degeneration of brain white matter (WM) in aging is a well-recognized problem, its quantification has mainly relied on volumetric measurements, which lack detail in describing the degenerative adaptation. In this study, WM structural complexity was evaluated in healthy old and young adults by analyzing the three-dimensional fractal dimension (FD) of WM segmented from magnetic resonance images of brain. FDs detected in the old were significantly smaller than in the young subjects. Specifically, WM interior structure complexity degenerated in the left hemisphere in old men but in the right hemisphere in old women. Men showed more complex WM patterns than women. An asymmetrical (right-greater-than-left-hemisphere) complexity pattern was observed in the interior and general structures of WM, yet the surface complexity was symmetrical across WM structures of the two hemispheres. WM volumes were also measured, but no significant decline was found with aging. These results suggest that the deterioration of WM complexity is not uniformly distributed between the genders and across brain hemispheres.

Adolescent↗
PubMed2006

Long-term prevention of pressure ulcers in high-risk patients: a single case study of the use of gluteal neuromuscular electric stimulation.

OBJECTIVE: To evaluate the efficacy of gluteal neuromuscular electric stimulation (NMES) using implanted percutaneous electrodes to improve regional tissue health and decrease the risk of pressure ulcer development. DESIGN: Case study of long-term use of gluteal NMES. SETTING: Community. PARTICIPANT: A patient with a C4-level American Spinal Injury Association grade A spinal cord injury, 22 years postinjury at study enrollment, and a clinical history of regular grade II and occasional IV ischial pressure ulcers. INTERVENTION: Gluteal NMES using an electric stimulation system comprising a combination of implanted percutaneous electrodes and an external stimulator (controller). MAIN OUTCOME MEASURES: Objective measurements of tissue health comprising evaluation of gluteal muscle thickness, interface pressures, and regional blood flow. Subjective self-reported sitting tolerance. RESULTS: Increased gluteal muscle thickness and blood flow together with reduced regional interface pressures occurred. Weight-shifting because of alternating left and right gluteal NMES became more effective over time as the muscles strengthened. Sitting tolerance more than doubled. CONCLUSIONS: A gluteal NMES system has been developed that provides both improved regional tissue health and dynamic weight shifting while seated in the wheelchair. In the current case, regular daily use had a positive impact on multiple indirect indicators of tissue health. Continued use was indicated as the positive effects were lost when stimulation was discontinued.

Adult↗
PubMed2006

Reliability of electronic versus manual wound measurement techniques.

OBJECTIVE: To compare the accuracy and reliability of 3 wound measurement techniques, including linear and 2 electronic techniques--Visitrak and the VeV MD system. DESIGN: Repeated measures involving forty 2-dimensional "wounds" with a range of clinically relevant sizes were created using regular paper. Blinded observers measured the surface areas of wounds in 2 sessions, using 3 techniques. SETTING: Research department of a tertiary referral center. PARTICIPANTS: Four blinded observers. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURES: Mixed linear models were fitted to determine interobserver and intraobserver variability. The average root mean square error (RMSE) for each measurement technique was determined to investigate the accuracy. RESULTS: Intraobserver variation was not significant in most measurement techniques. Interobserver variation was significant for all techniques. Linear measurements showed the highest RMSE, whereas VeV and Visitrak were comparable. CONCLUSIONS: Reliability of repeated wound measurements for all techniques can be achieved only with the same observer. Linear measurement has the least accuracy in evaluating wound size, VeV is slightly better than Visitrak for large wounds, and Visitrak is slightly better than VeV for small wounds. Our study shows that the use of electronic devices is superior to manual techniques to achieve valid measurements of wound area.

Humans↗
PubMed2006

Proteomic identification of potential target proteins regulated by an ASK1-mediated proteolysis pathway.

The ASK1 (ARABIDOPSIS SKP1-LIKE) protein is a critical component of the SCF (Skp1-Cullin-F box protein) ubiquitin ligase complexes that recruit target proteins for degradation by the 26S proteosome. To investigate proteins that are affected by the ASK1-mediated proteolysis pathway in Arabidopsis flowers, we compared the proteomes of the Arabidopsis wild type and ask1 mutant flower buds using two-dimensional electrophoresis (2-DE). Ten protein spots with higher or lower abundance in the ask1 mutant flowers compared to wild type flowers were excised and subjected to further mass spectrometry (MS) analysis. The results showed that they were proteins involved in photomorphogenesis, circadian oscillation, post-translation process, stress-responses and cell expansion or elongation, suggesting that those processes were affected in the ask1 mutant. The transcript levels of these genes were also compared based on the Affymetrix gene chip microarray data. No significant difference was observed for most of the genes, suggesting that the proteins with elevated levels of accumulation in the ask1 mutant could be candidate targets regulated by an ASK1-mediated proteolysis pathway. These results help to elucidate the pleiotropic functions of ASK1 in Arabidopsis developmental processes and also demonstrate the importance and necessity of studying protein levels with respect to gene functions.

Arabidopsis↗
PubMed2005

Fatigue induces greater brain signal reduction during sustained than preparation phase of maximal voluntary contraction.

Animal studies have shown that there are cell populations only discharging phasically before a motor task and others only active tonically during holding phase of the task. How muscle fatigue influences these two types of cell populations, however, is unknown. Because the phasic neurons are only active briefly before the task but the tonic ones are active continuously throughout the task, we hypothesized that fatigue would have a less effect on cortical signals during the preparation phase (representing phasic discharge) than that during the sustained phase (representing tonic discharge). Eight participants performed 200 handgrip maximal voluntary contractions (MVCs) with simultaneous recordings of scalp electroencephalographic (EEG), handgrip force, and finger flexor surface electromyographic (EMG) signals. Power spectrograms of the EEG during the preparation and sustained phases were analyzed in each of the five 40-trial blocks, with data from the first block representing a condition of moderate fatigue and the last, severe fatigue. Movement-related cortical potential (MRCP) was derived by trigger-averaging 40 EEG epochs in each block. The power of all EEG frequencies did not alter significantly during the preparation phase but decreased significantly during the sustained phase of the contraction. The MRCP negative potential (NP) related to motor task preparation only showed minimal changes. These results suggest that MVC-induced fatigue has differential effects on cortical signals during motor task preparation compared to its execution and maintenance. The signals of the two phases may represent activities of the two cortical cell populations previously found by animal studies.

Adult↗
PubMed2005

Identification and functional analysis of in vivo phosphorylation sites of the Arabidopsis BRASSINOSTEROID-INSENSITIVE1 receptor kinase.

Brassinosteroids (BRs) regulate multiple aspects of plant growth and development and require an active BRASSINOSTEROID-INSENSITIVE1 (BRI1) and BRI1-ASSOCIATED RECEPTOR KINASE1 (BAK1) for hormone perception and signal transduction. Many animal receptor kinases exhibit ligand-dependent oligomerization followed by autophosphorylation and activation of the intracellular kinase domain. To determine if early events in BR signaling share this mechanism, we used coimmunoprecipitation of epitope-tagged proteins to show that in vivo association of BRI1 and BAK1 was affected by endogenous and exogenous BR levels and that phosphorylation of both BRI1 and BAK1 on Thr residues was BR dependent. Immunoprecipitation of epitope-tagged BRI1 from Arabidopsis thaliana followed by liquid chromatography-tandem mass spectrometry (LC/MS/MS) identified S-838, S-858, T-872, and T-880 in the juxtamembrane region, T-982 in the kinase domain, and S-1168 in C-terminal region as in vivo phosphorylation sites of BRI1. MS analysis also strongly suggested that an additional two residues in the juxtamembrane region and three sites in the activation loop of kinase subdomain VII/VIII were phosphorylated in vivo. We also identified four specific BAK1 autophosphorylation sites in vitro using LC/MS/MS. Site-directed mutagenesis of identified and predicted BRI1 phosphorylation sites revealed that the highly conserved activation loop residue T-1049 and either S-1044 or T-1045 were essential for kinase function in vitro and normal BRI1 signaling in planta. Mutations in the juxtamembrane or C-terminal regions had only small observable effects on autophosphorylation and in planta signaling but dramatically affected phosphorylation of a peptide substrate in vitro. These findings are consistent with many aspects of the animal receptor kinase model in which ligand-dependent autophosphorylation of the activation loop generates a functional kinase, whereas phosphorylation of noncatalytic intracellular domains is required for recognition and/or phosphorylation of downstream substrates.

Arabidopsis↗
PubMed2005

Synthesis and fluorescence studies of thiazole orange tethered onto oligonucleotide: development of a self-contained DNA biosensor on a fiber optic surface.

Thiazole orange dyes were derivatized with ethylene glycol linkers of various lengths, and were covalently linked to the 5' end of the oligonucleotides after solid-phase synthesis. The labeled oligonucleotides exhibited enhanced fluorescence upon hybridization to complementary DNA sequences at the surfaces of optical fibers, providing for a self-contained labeling strategy. It was determined that the melt temperatures of DNA hybrids using one mixed polypyrimidine base oligonucleotide sequence were dependent on the length of the tethers, and that the melt temperature could be shifted by more than 10 degrees C when tethers were introduced.

Base Sequence↗
PubMed2005

Interaction of Arabidopsis BRASSINOSTEROID-INSENSITIVE 1 receptor kinase with a homolog of mammalian TGF-beta receptor interacting protein.

Brassinosteroids (BRs) regulate multiple aspects of plant growth and development and require an active BRASSINOSTEROID-INSENSITIVE 1 (BRI1) receptor serine/threonine kinase for hormone perception and signal transduction. In mammals, the transforming growth factor-beta (TGF-beta) family of polypeptides modulate numerous aspects of development and are perceived at the cell surface by a complex of type I and type II TGF-beta receptor serine/threonine kinases. TGF-beta receptor interacting protein (TRIP-1) is a cytoplasmic substrate of the TGF-beta type II receptor kinase and plays a role in TGF-beta signaling. TRIP-1 is a WD domain protein that also functions as an essential subunit of the eIF3 eukaryotic translation initiation factor in animals, yeast and plants. We previously cloned putative TRIP-1 homologs from bean and Arabidopsis and found that transgenic Arabidopsis plants expressing antisense TRIP-1 RNA exhibited a broad range of developmental defects including some morphological characteristics that resemble the phenotype of BR-deficient and -insensitive mutants. We now show that the BRI1 kinase domain phosphorylates Arabidopsis TRIP-1 on three specific sites in vitro (Thr-14, Thr-89 and either Thr-197 or Ser-198). Co-immunoprecipitation experiments using antibodies against TRIP-1, BRI1 and various fusion proteins strongly suggest that TRIP-1 and BRI1 also interact directly in vivo. These findings support a role for TRIP-1 in the molecular mechanisms of BR-regulated plant growth and development, possibly as a cytoplasmic substrate of the BRI1 receptor kinase.

Amino Acid Sequence↗
PubMed2005

Brome mosaic virus 1a nucleoside triphosphatase/helicase domain plays crucial roles in recruiting RNA replication templates.

Positive-strand RNA virus RNA replication is invariably membrane associated and frequently involves viral proteins with nucleoside triphosphatase (NTPase)/helicase motifs or activities. Brome mosaic virus (BMV) encodes two RNA replication factors: 1a has a C-terminal NTPase/helicase-like domain, and 2a(pol) has a central polymerase domain. 1a accumulates on endoplasmic reticulum membranes, recruits 2a(pol), and induces 50- to 70-nm membrane invaginations (spherules) serving as RNA replication compartments. 1a also recruits BMV replication templates such as genomic RNA3. In the absence of 2a(pol), 1a dramatically stabilizes RNA3 by transferring RNA3 to a membrane-associated, nuclease-resistant state that appears to correspond to the interior of the 1a-induced spherules. Prior results show that the 1a NTPase/helicase-like domain contributes to RNA recruitment. Here, we tested mutations in the conserved helicase motifs of 1a to further define the roles of this domain in RNA template recruitment. All 1a helicase mutations tested showed normal 1a accumulation, localization to perinuclear endoplasmic reticulum membranes, and recruitment of 2a(pol). Most 1a helicase mutants also supported normal spherule formation. Nevertheless, these mutations severely inhibited RNA replication and 1a-induced stabilization of RNA3 in vivo. For such 1a mutants, the membrane-associated RNA3 pool was both reduced and highly susceptible to added nuclease. Thus, 1a recruitment of viral RNA templates to a membrane-associated, nuclease-resistant state requires additional functions beyond forming spherules and recruiting RNA to membranes, and these functions depend on the 1a helicase motifs. The possibility that, similar to some double-stranded RNA viruses, the 1a NTPase/helicase-like domain may be involved in importing viral RNAs into a preformed replication compartment is discussed.

Bromovirus↗
PubMed2004

Identification and characterization of proteins that interact with the carboxy terminus of poly(A)-binding protein and inhibit translation in vitro.

Poly(A)-binding proteins (PABPs) are multifunctional proteins that play important roles in mRNA stability and protein translation. Two cucumber ( Cucumis sativus L.) proteins, PCI6 (PABP-CT-interacting) and PCI243 were identified based on ability to interact with the carboxy terminus (CT) of PABP in yeast two-hybrid and in vitro binding assays. PCI6 and PCI243 share a conserved amino acid domain (SxLnpnApxFxP) in common with human PABP-CT interactors, and with Arabidopsis ERD15 (early-responsive to dehydration). Deletion analysis and point mutations indicate that presence of this domain is necessary for the interaction, and tests with ERD15 demonstrate that it is predictive of interaction. Other plant proteins possessing this domain fall into two categories: small, acidic proteins like PCI6, PCI243 and ERD15, and larger neutral proteins that also include an RNA recognition motif. PCI6 is expressed in a range of tissues, e.g., leaves, roots, stems and flowers, and follows a diurnal pattern of expression, increasing during light hours and declining overnight. In wheat germ and mouse ascites Krebs-2 in vitro translation systems, PCI6 inhibited translation whereas the non-interacting mutant, PCI6-23A, did not or had a greatly reduced effect. The activity of PCI6, therefore, is reminiscent of that of human PABP-interacting protein 2 (Paip2). These results demonstrate a novel interaction between PABP and several plant proteins sharing a SxLnpxApxFxP motif, with possible implications for translational regulation.

Amino Acid Sequence↗
PubMed2003

[Expressions of MAD2 and p55CDC in prostate cancer and their correlations with the prostate cancer grading].

OBJECTIVE: To investigate if downregulation of two mitotic checkpoint proteins, MAD2 and p55CDC, is a frequent event in human prostate cancer and whether decreased expression of these two proteins are associated with progression of prostate cancer. METHODS: Using immunohistochemistry technique, the expressions of MAD2 and p55CDC proteins are examined in 46 benign prostate hyperplasia (BPH) and 65 prostate cancer tissues. Differential expressions were compared first between BPH and prostate cancer specimens, and then among prostate cancer samples with different Gleason grades. RESULTS: We found that down-regulation of MAD2 and p55CDC expressions was significant in prostate cancer (96% and 83%, respectively) compared to BPH (19.5% and 4.3%, respectively) (P<0.001). In addition, decreased expression levels of these two proteins were associated with increased Gleason grade. CONCLUSION: Our results indicate that loss of MAD2 and p55CDC protein expression is a frequent event in prostate carcinoma and the decreased expressions of these two proteins are associated with increased Gleason grade. Our results provide first in vivo evidence to support the hypothesis that down regulation of certain mitotic checkpoint proteins plays an important part in human tumourigenesis.

Calcium-Binding Proteins↗