Biomedical subjects

Yan Fu

Publications and source records attributed to Yan Fu.

At least 19 recordsLinked to original sources

PubMed2026

Contrasting redox-related physiological responses associated with HaGATA23 and HaGATA36 during Orobanche cumana parasitism in sunflower (Helianthus annuus L.).

Helianthus annuus is an economically important Asteraceae species used for seed oil production and ornamental purposes, but its production is seriously affected by the root-parasitic plant Orobanche cumana. GATA transcription factors are zinc-finger DNA-binding regulators involved in plant development and stress adaptation. However, the molecular characteristics of GATA transcription factors in Helianthus annuus and their contribution to Helianthus annuus -Orobanche cumana interaction remain poorly understood. Here, 36 HaGATA members were retrieved from the Helianthus annuus genome and classified into four phylogenetic clades. Chromosomal placement, collinearity, gene structure, motif composition, and promoter elements varied among the 36 HaGATA members, indicating evolutionary conservation coupled with functional diversification. Expression analysis and RT-qPCR analyses revealed differential expression patterns among HaGATA genes under O. cumana stress, with HaGATA23 markedly downregulated and HaGATA36 strongly upregulated. Overexpression of HaGATA23 was associated with increased malondialdehyde (MDA) accumulation and unfavorable changes in antioxidant enzyme activities, whereas its silencing showed the opposite physiological tendency. In contrast, overexpression of HaGATA36 reduced malondialdehyde accumulation, increased peroxidase (POD), catalase (CAT), and superoxide dismutase (SOD) activities, while its silencing showed the reverse tendency. These results indicate that HaGATA23 and HaGATA36 are candidate genes associated with contrasting redox-related physiological responses during O. cumana stress. This work provides evidence that GATA transcription factors are associated with redox-related physiological responses in sunflower under O. cumana treatment and identifies HaGATA23 and HaGATA36 as functionally divergent candidate genes for further validation.

Helianthus↗

PubMed2026

AI proteomics: from protein identification to virtual cells.

Artificial intelligence (AI) is transforming scientific research, including proteomics. In this Perspective, we highlight key mass spectrometry (MS)-based proteomics areas where AI is driving innovation, ranging from protein identification to building AI virtual cells. These include improving peptide and protein identification and quantification; characterizing protein-protein interactions and protein complexes; advancing spatial and perturbation proteomics; integrating multi-omics data; and, ultimately, enabling AI virtual cells. Finally, we call for global collaboration among data producers, data consumers and other stakeholders to establish an AI-friendly ecosystem for MS-based proteomics, laying the foundation for transformative advancements in proteomics driven by AI.

Proteomics↗

PubMed2007

Mitochondrial DNA distinction of northeastern China roe deer, Siberian roe deer, and European roe deer, to clarify the taxonomic status of northeastern China roe deer.

Partial sequences of the mitochondrial control region of northeastern China roe deer were analyzed to determine the degree of genetic diversity. Fourteen haplotypes were observed. The haplotype diversity was high (h = 0.872), nucleotide diversity was medium (p ( i ) = 0.0108), and the average Tamura-Nei nucleotide distance among them was 1.9%, indicating that genetic diversity of roe deer from northeastern China was relatively high and that the effective population size was large historically. To clarify the northeastern China roe deer's taxonomic status, these 14 haplotypes were compared with 31 haplotypes published in Genbank from Europe, Siberia, and Korea. The average genetic distance between haplogroups of northeastern China and European roe deer (5.8%) was more than twice that between northeastern China and Siberian roe deer (2.7%), indicating sufficient variation to consider roe deer of northeastern China and Siberia as a single species (Capreolus pygargus), distinct from European roe deer (Capreolus capreolus). This is the first presentation of mtDNA data for roe deer in northeastern China, which will be helpful in investigations of genetic diversity and clarifications of the taxonomic status of roe deer in the whole of China.

Animals↗

PubMed2007

Analysis of polymorphism, structure and function of exon 2 of ovine melatonin receptor 1b gene: a clue as to why it lacks expression in sheep.

To analyze the structure and function of the melatonin 1b receptor (MT2) in sheep, single nucleotide polymorphisms were detected in exon 2 of sheep MT2 gene using genomic DNA from five sheep breeds by five primers. Polymorphisms were found, and 33 nucleotide mutations were revealed by comparing the mutant types with the wild types. Among them, 14 give rise to deduced amino acid changes. However, none is likely to be associated with nonseasonal or seasonal estrus in sheep breeds tested. Sequence of exon 2 of MT2 of Small Tail Han sheep shows much closer phylogenetic relationship with predicted bovine and porcine MT2 than with human and mouse. The deduced amino acid sequence shows higher identity with the MT2 of cattle (95%) and pig (79%) than with human (76%) and mouse (71%). A rather high identity (61-63%) with the MT1 of sheep, human and mouse was also found. Compared with the other known MT2, 35 unique altered amino acids were revealed. Albeit it also contains a NAXXY motif in transmembrane 7, both a DRY motif and a CYVCR motif were detected just downstream from its third transmembrane domain rather than NRY and CYICH found in other melatonin receptor groups. We presumed that it is possible that the structural changes make its binding function to the ligands attenuated or disrupted, and other genes (most probably MT1) were substituted in the progress of evolution, which ultimately resulted in no detectable expression in current breeds of sheep.

Amino Acid Sequence↗

PubMed2006

[Calreticulin expression increases during delayed cardioprotection induced by hypoxic preconditioning].

Both in vivo and cultured cardiomyocyte experiments were performed to investigate the alteration of expression of calreticulin (CRT) during the delayed cardioprotection induced by hypoxic preconditioning (HPC) and the intracellular signal transduction mechanisms of the alteration. (1) Wistar rats were randomly divided into three groups: sham operation group (Sham), myocardial infarction (MI) group induced by left coronary artery ligation and HPC+MI group (4-hour HPC 24 h before MI). Twenty-four hours, 14 d and 28 d after left coronary artery ligation, myocardial function, infarction size and the area at risk were measured. Western blot was used to detect the expression of CRT, the activity of p38 mitogen-activated protein kinase (MAPK) and stress-activated protein kinase (SAPK). (2) Cultured cardiomyocytes from neonatal Sprague-Dawley (SD) rat were divided into six groups: hypoxia/reoxygenation (H/R), HPC, HPC+H/R, p38 MAPK inhibitor SB203580+HPC+H/R (SB+HPC+H/R), SAPK inhibitor SP600125+HPC+H/R (SP+HPC+H/R) and control. Survival rate and apoptosis rate of cardiomyocytes 6 h after H/R and activities of lactate dehydrogenase (LDH) in culture medium in each group were measured. Western blot was used to detect the expression of CRT and activities of p38 MAPK and SAPK. The results are as follows: (1) During in vivo experiment, compared with MI group, HPC significantly improved +dp/dt(max) and -dp/dt(max), reduced infarction size and the area at risk. HPC dramatically changed the expression of CRT. CRT expression in HPC+MI group was 206% of that in MI group (P<0.05) 24 h after infarction, especially in the area at risk. However, 28 d after operation, the expression of CRT decreased by 57%. Correlation analysis indicated a positive correlation between CRT expression and myocardial function (r=0.9867, P<0.05), and negative correlation between CRT expression and infarction size (r=-0.9709, P<0.05). (2) In cultured cardiomyocytes, HPC attenuated cell injury induced by H/R. CRT expression increased moderately to 222% of control (P<0.05) during HPC, but increased dramatically to 503% of control (P<0.05) after H/R. HPC reduced H/R-induced CRT up-regulation to 56% of that in H/R group (P<0.05). Correlation analysis indicated that CRT expression induced by HPC had a positive correlation with p38 MAPK activity (r=0.9021, P<0.05), but a negative correlation with SAPK activity (r=-0.8211, P<0.05). Both in vivo and in vitro results indicate that HPC protects myocardium from ischemia or H/R injury. p38 MAPK is possibly involved in the up-regulation of CRT induced by HPC, while SAPK has a negative influence.

Animals↗

PubMed2006

Nearly identical paralogs: implications for maize (Zea mays L.) genome evolution.

As an ancient segmental tetraploid, the maize (Zea mays L.) genome contains large numbers of paralogs that are expected to have diverged by a minimum of 10% over time. Nearly identical paralogs (NIPs) are defined as paralogous genes that exhibit > or = 98% identity. Sequence analyses of the "gene space" of the maize inbred line B73 genome, coupled with wet lab validation, have revealed that, conservatively, at least approximately 1% of maize genes have a NIP, a rate substantially higher than that in Arabidopsis. In most instances, both members of maize NIP pairs are expressed and are therefore at least potentially functional. Of evolutionary significance, members of many NIP families also exhibit differential expression. The finding that some families of maize NIPs are closely linked genetically while others are genetically unlinked is consistent with multiple modes of origin. NIPs provide a mechanism for the maize genome to circumvent the inherent limitation that diploid genomes can carry at most two "alleles" per "locus." As such, NIPs may have played important roles during the evolution and domestication of maize and may contribute to the success of long-term selection experiments in this important crop species.

Arabidopsis↗

PubMed2006

Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize.

A new genetic map of maize, ISU-IBM Map4, that integrates 2029 existing markers with 1329 new indel polymorphism (IDP) markers has been developed using intermated recombinant inbred lines (IRILs) from the intermated B73xMo17 (IBM) population. The website http://magi.plantgenomics.iastate.edu provides access to IDP primer sequences, sequences from which IDP primers were designed, optimized marker-specific PCR conditions, and polymorphism data for all IDP markers. This new gene-based genetic map will facilitate a wide variety of genetic and genomic research projects, including map-based genome sequencing and gene cloning. The mosaic structures of the genomes of 91 IRILs, an important resource for identifying and mapping QTL and eQTL, were defined. Analyses of segregation data associated with markers genotyped in three B73/Mo17-derived mapping populations (F2, Syn5, and IBM) demonstrate that allele frequencies were significantly altered during the development of the IBM IRILs. The observations that two segregation distortion regions overlap with maize flowering-time QTL suggest that the altered allele frequencies were a consequence of inadvertent selection. Detection of two-locus gamete disequilibrium provides another means to extract functional genomic data from well-characterized plant RILs.

Alleles↗

PubMed2006

Design, synthesis, and evaluation of Leu*Ala hydroxyethylene-based non-peptide beta-secretase (BACE) inhibitors.

With the aim of developing small molecular non-peptide beta-secretase (BACE) inhibitors, Leu*Ala hydroxyethylene (HE) was investigated as a scaffold to design and synthesize a series of compounds. Taking advantage of efficient combinatorial synthesis approaches and molecular modeling, extensive structure-activity relationship (SAR) studies were carried out on the N- and C-terminal residues of the Leu*Ala HE scaffold. Isobutyl amine was found to be an optimal C-cap, and suitable hydroxylalkylamines at the 3-position and nitro or methyl(methylsulfonyl)amine at the 5-position of isophthalamide as the N-terminus could form additional hydrogen bonds with BACE active sites and help improve potency. Many new potent non-peptide BACE inhibitors were identified in this study. Among them, compounds 37 and 44 exhibited excellent enzyme-inhibiting potency, comparable to that of OM99-2, and obvious inhibitory effects in cell-based assay with low molecular weights (<600).

Amyloid Precursor Protein Secretases↗

PubMed2006

Calreticulin induces delayed cardioprotection through mitogen-activated protein kinases.

Hypoxic preconditioning (HPC) attenuates tissue injury caused by ischemia/reperfusion. The protective mechanisms of HPC involve up-regulation of the protective proteins and mitigation of cellular calcium overload. Calreticulin (CRT), a Ca(2+)-binding chaperone, plays an important role in regulating calcium homeostasis and folding of proteins. The role of CRT in cardioprotection of HPC and the pathways determining CRT expression during HPC are not clear. In this work, 2-DE and MALDI-MS were employed to analyze CRT differential expression in cardiomyocytes subjected to transient hypoxia. Western blotting analysis was used to detect the CRT expression and activities of p38 mitogen-activated protein kinase (p38 MAPK) and c-Jun NH(2)-terminal kinase (JNK) in myocardium subjected to ischemia with and without HPC and sham operation. The hearts from HPC group were more resistant to sustained ischemia and had much stronger phosphorylation of p38 MAPK, with a reduced phosphorylation of JNK, than controls. The CRT expression was positively correlated with the phosphorylation of p38 MAPK and negatively correlated with the level of JNK phosphorylation. Furthermore, inhibition of the p38 MAPK with SB202190 abolished, while inhibition of the JNK with SP600125 enhanced the CRT up-regulation in cardiomyocytes induced by HPC. The results indicate that HPC up-regulates CRT expression through the MAPK signaling pathways.

Animals↗

PubMed2006

Gene expression profiling in porcine mammary gland during lactation and identification of breed- and developmental-stage-specific genes.

A total of 28941 ESTs were sequenced from five 5'-directed non-normalized cDNA libraries, which were assembled into 2212 contigs and 5642 singlets using CAP3. These sequences were annotated and clustered into 6857 unique genes, 2072 of which having no functional annotations were considered as novel genes. These genes were further classified into Gene Ontology categories. By comparing the expression profiles, we identified some breed- and developmental-stage-specific gene groups. These genes may be relative to reproductive performance or play important roles in milk synthesis, secretion and mammary involution. The unknown EST sequences and expression profiles at different developmental stages and breeds are very important resources for further research.

Animals↗

PubMed2006

Identification of cold acclimation-responsive Rhododendron genes for lipid metabolism, membrane transport and lignin biosynthesis: importance of moderately abundant ESTs in genomic studies.

We have previously analysed expressed sequence tags (ESTs) from non-acclimated (NA) and cold-acclimated (CA) Rhododendron leaves, and identified highly abundant complementary DNAs (cDNAs) possibly involved in cold acclimation. A potentially significant, but relatively unexplored, application of these EST data sets is the study of moderately abundant cDNAs, such as those picked only 1-3 times from each Rhododendron EST library containing approximately 430 ESTs. Using statistical tests and Northern blots, we established that the probability of differential expression of moderately abundant cDNAs based on the EST data is, indeed, a reasonably accurate predictor of their 'true' upregulation or downregulation as 11 out of 13 cDNAs (85%) studied fit this criterion. The analyses also revealed four aspects of cold acclimation in Rhododendron leaf tissues. Firstly, the concomitant upregulation of long-chain acyl-coenzyme A (acyl-CoA) synthetase, CTP:cholinephosphate cytidylyltransferase and delta-12 fatty acid desaturase in CA leaf tissues suggests that phospholipid biosynthesis and desaturation are important components of cold hardening in Rhododendron. Secondly, upregulation of plastidic nicotinamide adenine dinucleotide phosphatemalic enzyme (NADP-ME) in CA tissues suggests that malate is an important source of acetyl-CoA used for fatty acid biosynthesis during cold acclimation. Thirdly, down-regulation of plasma membrane intrinsic protein (PIP)2-1 aquaporin and upregulation of gated outward rectifying K+ channel (GORK) in CA tissues may be associated with the protection of overwintering leaves from freeze-induced cellular dehydration. Fourthly, upregulation of coumarate 3-hydroxylase may be associated with cell wall thickening in CA tissues. Physiological implications of these results, which reveal potentially novel regulations of cold acclimation in overwintering woody evergreens, are discussed. This work highlights the importance of also investigating low/moderately abundant ESTs (in addition to highly abundant ones) in genomic studies, in that it offers an effective strategy for identifying stress-related genes, especially when large-scale cDNA sequencing/microarray studies are not possible.

Acclimatization↗

PubMed2006

Association of CYP2D6 and CYP1A2 gene polymorphism with tardive dyskinesia in Chinese schizophrenic patients.

AIM: To investigate the possible association of the CYP2D6 gene C100T polymorphism and the CYP1A2 gene C163A polymorphism with tardive dyskinesia (TD) in Chinese patients with schizophrenia. METHODS: The recruited schizophrenic patients were assessed with the Abnormal Involuntary Movement Scale (AIMS), and divided into groups with TD (n=91) and without TD (n=91) according to the AIMS score. Polymorphisms of the CYP2D6 and CYP1A2 genes were determined by polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP). RESULTS: No allele frequencies deviated from Hardy-Weinberg equilibrium. No significant differences in genotypes frequencies of the CYP2D6 C100T polymorphism were observed between patients with TD and without TD (Chi2=4.078, P>0.05), but patients with TD had a significant excess of the T allele compared with those without TD (Chi2=4.28, P<0.05). Moreover, the frequency of the CYP1A2 C allele in patients with TD was significantly higher than that in those without TD (Chi2=6.38, P<0.05). An association between TD and the CYP2D6 100T and CYP1A2 163C alleles was observed. Additionally, there were no differences in the mean AIMS scores among different genotypes in TD patients as a group or in smokers. The results of logistic regression analysis demonstrated that mean age and duration of illness were risk factors for TD, but not sex, cumulative exposure to neuroleptic drugs in years, CYP2D6 or CYP1A2 genotype. CONCLUSION: The C100T polymorphism of the CYP2D6 gene and the C163A polymorphism of the CYP1A2 gene may be associated with neuroleptic drug-induced tardive dyskinesia in Chinese patients with schizophrenia. However, genetic factors have a weaker association with susceptibility to TD compared with mean age and duration of illness.

Age Factors↗

PubMed2006

[Experimental study on the survival of venous flap with different pedicle styles].

OBJECTIVE: To study a new method of venous flap that is improved on its persistence and quality. METHODS: New Zealand white rabbits were subdivided randomly into 4 groups. All rabbits were operated by harvesting a flap from the latero-abdominal wall and then sutured it in the original position. Group A: the superficial epigastric vein in the pedicle was left open (only one inflow vein remained). Group B: the pedicle vein of the proximal and distant end were left open (keeping an inflow vein and a principal out). Group C: the pedicle vein and a tributary vein were left open (keeping an inflow vein and a tributary outflow vein). Group D: the pedicle vein and two tributary veins were left open (keeping an inflow vein and two tributary outflow veins). Survival rate, MDA of the tissue, histology and ultra-microstructure were examined. RESULTS: Survival rate of A, B, C, D were improved in order. Statistic difference is significant (P < 0.05) between group and group other than C and D. The content of MDA was heightened with statistically significant differences (A > B > C > D) among the four groups 8 hours postoperatively, but fell back to the normal level in group D and C and kept a high level in group A and B at 72 hour postoperatively. Histology and ultra-microstructure exam showed that degeneration of collagen fiber and karyopyknosis of cell is more obvious in Group A and Group B than Group C and Group D. CONCLUSIONS: The higher survival rate of venous flap is possible by designing the more reasonable venous flap outputs pedicles which can alleviate the high tension dropsy and maintain the valid equilibrium of pour with flow in the venous flap.

Animals↗

PubMed2006

An SVM scorer for more sensitive and reliable peptide identification via tandem mass spectrometry.

Tandem mass spectrometry (MS/MS) has become increasingly important and indispensable in high-throughput proteomics for identifying complex protein mixtures. Database searching is the standard method to accomplish this purpose. A key sub-routine, peptide identification, is used to generate a list of candidate peptides from a protein database according to an experimental MS/MS spectrum, and then validate these candidate peptides for protein identification. Although currently there are many algorithms for peptide identification, most of them either lack an effective validation module or only validate the first-ranked peptide, thus leading to a low identification reliability or sensitivity. This paper proposes a new algorithm, named pepReap, to overcome the above drawbacks. It consists of a two-layered scoring scheme based on machine learning. The first layer is a rough scoring function which uses some simple and heuristic factors to measure the degree of the matches between an experimental MS/MS spectrum and the candidate peptides; thus a ranked list of candidate peptides is generated at a relatively low computational cost. The second layer is a fine scoring function which re-ranks the candidate peptides generated in the first layer and determines which one among them is the true positive. The fine scoring function was designed based on support vector machines (SVMs) using more comprehensive factors, such as the correlations between ions, the mass matching errors of fragment and peptide ions, etc. Consequently, the SVM classifier serves as not only a scorer but also a validation module. Experimental comparison with the popular SEQUEST algorithm coupled with threshold validation criteria on a reported dataset demonstrates that the pepReap algorithm achieves higher performance in terms of identification sensitivity with comparable precision.

Algorithms↗

PubMed2005

Intron-flanking EST-PCR markers: from genetic marker development to gene structure analysis in Rhododendron.

With a long-term goal of constructing a linkage map of Rhododendron enriched with gene-specific markers, we utilized Rhododendron catawbiense ESTs for the development of high-efficiency (in terms of generating polymorphism frequency) PCR-based markers. Using the gene-sequence alignment between Rhododendron ESTs and the genomic sequences of Arabidopsis homologs, we developed 'intron-flanking' EST-PCR-based primers that would anneal in conserved exon regions and amplify across the more highly diverged introns. These primers resulted in increased efficiency (61% vs. 13%; 4.7-fold) of polymorphism-detection compared with conventional EST-PCR methods, supporting the assumption that intron regions are more diverged than exons. Significantly, this study demonstrates that Arabidopsis genome database can be useful in developing gene-specific PCR-based markers for other non-model plant species for which the EST data are available but genomic sequences are not. The comparative analysis of intron sizes between Rhododendron and Arabidopsis (made possible in this study by aligning of Rhododendron ESTs with Arabidopsis genomic sequences and the sequencing of Rhododendron genomic PCR products) provides the first insight into the gene structure of Rhododendron.

Arabidopsis↗

PubMed2005

Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes.

Recent sequencing efforts have targeted the gene-rich regions of the maize (Zea mays L.) genome. We report the release of an improved assembly of maize assembled genomic islands (MAGIs). The 114,173 resulting contigs have been subjected to computational and physical quality assessments. Comparisons to the sequences of maize bacterial artificial chromosomes suggest that at least 97% (160 of 165) of MAGIs are correctly assembled. Because the rates at which junction-testing PCR primers for genomic survey sequences (90-92%) amplify genomic DNA are not significantly different from those of control primers ( approximately 91%), we conclude that a very high percentage of genic MAGIs accurately reflect the structure of the maize genome. EST alignments, ab initio gene prediction, and sequence similarity searches of the MAGIs are available at the Iowa State University MAGI web site. This assembly contains 46,688 ab initio predicted genes. The expression of almost half (628 of 1,369) of a sample of the predicted genes that lack expression evidence was validated by RT-PCR. Our analyses suggest that the maize genome contains between approximately 33,000 and approximately 54,000 expressed genes. Approximately 5% (32 of 628) of the maize transcripts discovered do not have detectable paralogs among maize ESTs or detectable homologs from other species in the GenBank NR nucleotide/protein database. Analyses therefore suggest that this assembly of the maize genome contains approximately 350 previously uncharacterized expressed genes. We hypothesize that these "orphans" evolved quickly during maize evolution and/or domestication.

Chromosomes, Artificial, Bacterial↗

PubMed2005

Coherent anti-stokes Raman scattering imaging of axonal myelin in live spinal tissues.

We present a vibrational imaging study of axonal myelin under physiological conditions by laser-scanning coherent anti-Stokes Raman scattering (CARS) microscopy. We use spinal cord white matter strips that are isolated from guinea pigs and kept alive in oxygen bubbled Krebs' solution. Both forward- and epi-detected CARS are used to probe the parallel axons in the spinal tissue with a high vibrational contrast. With the CARS signal from CH2 vibration, we have measured the ordering degree and the spectral profile of myelin lipids. Via comparison with the ordering degrees of lipids in myelin figures formed of controlled lipid composition, we show that the majority of the myelin membrane is in the liquid ordered phase. By measuring the myelin thickness and axon diameter, the value of g ratio is determined to be 0.68 with forward- and 0.63 with epi-detected CARS. Detailed structures of the node of Ranvier and Schmidt-Lanterman incisure are resolved. We have also visualized the ordering of water molecules between adjacent bilayers inside the myelin. Our observations provide new insights into myelin organization, complementary to the knowledge from light and electron microscopy studies of fixed and dehydrated tissues. In addition, we have demonstrated simultaneous CARS imaging of myelin and two-photon excitation fluorescence imaging of intra- and extraaxonal Ca2+. The current work opens up a new approach to the study of spinal cord injury and demyelinating diseases.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2005

pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry.

SUMMARY: Research in proteomics requires powerful database-searching software to automatically identify protein sequences in a complex protein mixture via tandem mass spectrometry. In this paper, we describe a novel database-searching software system called pFind (peptide/protein Finder), which employs an effective peptide-scoring algorithm that we reported earlier. The pFind server is implemented with the C++ STL, .Net and XML technologies. As a result, high speed and good usability of the software are achieved.

Algorithms↗