Biomedical subjects

Bo Yan

Publications and source records attributed to Bo Yan.

At least 19 recordsLinked to original sources

PubMed2025

Gain-of-function PPM1D mutations attenuate ischemic stroke.

Identification of genetic aberrations in stroke, the second leading cause of death worldwide, is of paramount importance for understanding the disease pathogenesis and generating new therapies. Whole-genome sequencing from 10,241 ischemic stroke patients identified eight patients carrying gain-of-function mutations on coding variants in the protein phosphatase magnesium-dependent 1 δ (PPM1D) gene. Patients carrying PPM1D mutations exhibit better stroke-related clinical phenotypes, including improvements in peripheral inflammation, fibrinogen, low-density lipoprotein, cholesterol and plateletcrit level. Experimental brain ischemia in Ppm1d-deficient (Ppm1d-/-) mice resulted in enlarged lesions and pronounced neurological impairments. Spatial transcriptomics revealed a distinct Ppm1d-associated gene expression pattern, indicating disrupted endothelial homeostasis during ischemic brain injury. Proteomic analysis demonstrated that differentially expressed proteins in primary brain endothelial cells from Ppm1d-/- mice were significantly enriched in the peroxisome proliferator-activated receptors (PPARs)-mediated metabolic signaling. Mechanistically, Ppm1d deficiency promoted aberrant fatty acid β-oxidation and increased oxidative stress, which impaired endothelial cell function through the PPARα pathway. A small molecule, T2755, was identified to engage Trp427 and stabilize PPM1D, thereby mitigating ischemic brain injury in mice. Collectively, we find that PPM1D protects against ischemic brain injury and validates its pharmacological stabilizer T2755 as a promising therapy for ischemic stroke. Gain-of-function PPM1D mutations attenuate ischemic cerebral injury. Whole-genome sequencing data of 10,241 ischemic stroke patients from the Third Chinese National Stroke Registry (CNSR-III) identified eight patients with gain-of-function mutations in the protein phosphatase magnesium-dependent 1 δ (PPM1D) gene (17q23.2). These mutation carriers displayed improved peripheral inflammation, decreased fibrinogen, low-density lipoprotein, cholesterol and plateletcrit level. Ppm1d-deficient (Ppm1d-/-) mice exhibited exacerbated stroke outcomes, characterized by enlarged infarct volumes, disrupted cerebrovascular architecture, and enhanced neuro-inflammation. Mechanistically, Ppm1d deficiency induced the disturbance of endothelial fatty acid metabolism involving the PPARα pathway. Through integrated computational modeling, virtual screening, and in vitro validation, T2755 was identified as a small molecule PPM1D stabilizer. Pharmacological PPM1D stabilization with T2755 significantly attenuated ischemic brain injury in murine models.

Aged↗

PubMed2007

Noggin signaling from Xenopus animal blastomere lineages promotes a neural fate in neighboring vegetal blastomere lineages.

In Xenopus, localized factors begin to regionalize embryonic fates prior to the inductive interactions that occur during gastrulation. We previously reported that an animal-to-vegetal signal that occurs prior to gastrulation promotes primary spinal neuron fate in vegetal equatorial (C-tier) blastomere lineages. Herein we demonstrate that maternal mRNA encoding noggin is enriched in animal tiers and at low concentrations in the C-tier, suggesting that the neural fates of C-tier blastomeres may be responsive to early signaling from their neighboring cells. In support of this hypothesis, experimental alteration of the levels of Noggin from animal equatorial (B-tier) or BMP4 from vegetal (D-tier) blastomeres significantly affects the numbers of primary spinal neurons derived from their neighboring C-tier blastomeres. These effects are duplicated in blastomere explants isolated at cleavage stages and cultured in the absence of gastrulation interactions. Co-culture with animal blastomeres enhanced the expression of zygotic neural markers in C-tier blastomere explants, whereas co-culture with vegetal blastomeres repressed them. The expression of these markers in C-tier explants was promoted when Noggin was transiently added to the culture during cleavage/morula stages, and repressed with the transient addition of BMP4. Reduction of Noggin translation in B-tier blastomeres by antisense morpholino oligonucleotides significantly reduced the efficacy of neural marker induction in C-tier explants. These experiments indicate that early anti-BMP signaling from the animal hemisphere recruits vegetal equatorial cells into the neural precursor pool prior to interactions that occur during gastrulation.

Animals↗

PubMed2006

Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information.

We describe an improved artificial neural network (ANN)-based method for predicting peptide retention times in reversed-phase liquid chromatography. In addition to the peptide amino acid composition, this study investigated several other peptide descriptors to improve the predictive capability, such as peptide length, sequence, hydrophobicity and hydrophobic moment, and nearest-neighbor amino acid, as well as peptide predicted structural configurations (i.e., helix, sheet, coil). An ANN architecture that consisted of 1052 input nodes, 24 hidden nodes, and 1 output node was used to fully consider the amino acid residue sequence in each peptide. The network was trained using approximately 345,000 nonredundant peptides identified from a total of 12,059 LC-MS/MS analyses of more than 20 different organisms, and the predictive capability of the model was tested using 1303 confidently identified peptides that were not included in the training set. The model demonstrated an average elution time precision of approximately 1.5% and was able to distinguish among isomeric peptides based upon the inclusion of peptide sequence information. The prediction power represents a significant improvement over our earlier report (Petritis, K.; Kangas, L. J.; Ferguson, P. L.; Anderson, G. A.; Pasa-Tolic, L.; Lipton, M. S.; Auberry, K. J.; Strittmatter, E. F.; Shen, Y.; Zhao, R.; Smith, R. D. Anal. Chem. 2003, 75, 1039-1048) and other previously reported models.

Amino Acid Sequence↗

PubMed2006

Peptide sequence tag-based blind identification of post-translational modifications with point process model.

UNLABELLED: An important but difficult problem in proteomics is the identification of post-translational modifications (PTMs) in a protein. In general, the process of PTM identification by aligning experimental spectra with theoretical spectra from peptides in a peptide database is very time consuming and may lead to high false positive rate. In this paper, we introduce a new approach that is both efficient and effective for blind PTM identification. Our work consists of the following phases. First, we develop a novel tree decomposition based algorithm that can efficiently generate peptide sequence tags (PSTs) from an extended spectrum graph. Sequence tags are selected from all maximum weighted antisymmetric paths in the graph and their reliabilities are evaluated with a score function. An efficient deterministic finite automaton (DFA) based model is then developed to search a peptide database for candidate peptides by using the generated sequence tags. Finally, a point process model-an efficient blind search approach for PTM identification, is applied to report the correct peptide and PTMs if there are any. Our tests on 2657 experimental tandem mass spectra and 2620 experimental spectra with one artificially added PTM show that, in addition to high efficiency, our ab-initio sequence tag selection algorithm achieves better or comparable accuracy to other approaches. Database search results show that the sequence tags of lengths 3 and 4 filter out more than 98.3% and 99.8% peptides respectively when applied to a yeast peptide database. With the dramatically reduced search space, the point process model achieves significant improvement in accuracy as well. AVAILABILITY: The software is available upon request.

Algorithms↗

PubMed2006

[Expression of Merlin in cortex of temporal lobe and in hippocampal CA1 region of the Kindling Model of Epilepsy induced by corciaria lactone in rats].

OBJECTIVE: To explore the relationship between merlin and hippocampal sclerosis of temporal epilepsy. METHODS: The kindling model of epilepsy induced by corciaria lactone (CL) in rats was used. The expression of merlin in neuron of cortex of temporal lobe and hippocampal CA1 region was observed using immunohistochemistry method. Comparison of the amount of neuron with expression of merlin in the two locations was made between the kindled group, non-kindled group and control group. RESULTS: The expression of merlin in neuron of cortex of temporal lobe and hippocampal CA1 region of the kindled group was higher than the expression of the other two groups (P < 0.05), and there was no significant difference between the expression in the non-kindled group and that in the control group (P > 0.05). The expression of merlin in glial cell of the same region of all groups was seldom seen. CONCLUSION: The super-expression of merlin in neuron of cortex of temporal lobe and hippocampal CA1 region of the kindled rats may be involved in the process of neuronal apoptosis and hippocampal sclerosis.

Animals↗

PubMed2006

[Idiopathic sudden deafness: the therapeutic evaluation of hyperbaric oxygen treatment].

OBJECTIVE: To further evaluate the therapeutic effect of hyperbaric oxygen (HBO) to idiopathic sudden deafness. METHOD: A total number of 236 medical records of inpatients with idiopathic sudden deafness during 1997-2004 were collected from the Wuhan Union Hospital. Single factor analysis was done to evaluate the therapeutic effect with ten factors with SPSS analysis software. We divided the cases into HBO group and non-HBO group. The logistic regression was used in multivariate analysis. RESULT: Single factor analysis indicated that sex, ear side, presence of tinnitus, inducement and period of treatment had no effect on the prognosis, while age, course, presence of vertigo, a sensorineural hearing loss history with the other ear, degree of deafness had some effect on the prognosis. Multivariate analysis indicated: the effective (hearing threshold has elevated above 15 dB) ratio of HBO group comparing to the control group (non-HBO group), the difference was significant (P<0.01). CONCLUSION: The first visit after 14 days, the presence of vertigo, a sensorineural hearing loss history with the other ear and complete deafness may imply poor prognosis. HBO is effective for sudden deafness.

Adolescent↗

PubMed2006

[Using of titanium mesh for the reconstruction of skull base defect].

OBJECTIVE: The purpose of this study is to evaluate the possibility and surgical principle of titanium mesh used for the reconstruction of skull base bone defect. METHODS: The clinical data of 11 patients with defect of skull base bone repaired with titanium mesh were retrospectively analysed. RESULTS: Among 11 patients, there were 6 patients with skull base tumor, 3 patients with fibrosis hyperplasia, 2 patients with encephalomeningocele. The surgical approach included craniofacial approach in 7 patients, transfrontal and extended transfrontal approach in 3 patients, trans-midface approach in 1 patient. The anterior and lateral skull base was repaired in 2 patients, anterior and middle skull base and sellar repaired in 6 patients, anterior skull base and orbital floor repaired in 3 patients. In early postoperative period, there were 3 patients with intracranial pneumatosis, but without symptom, and 1 patient with transient cerebrospinal leakage. Following-up for average 14.4 months, there was no titanium mesh displacement and intracranial infection in all patients. CONCLUSIONS: The titanium mesh used for the repair of skull base bone defect was both possible and safe.

Adolescent↗

PubMed2006

Supercritical gasification for the treatment of o-cresol wastewater.

The supercritical water gasification of phenolic wastewater without oxidant was performed to degrade pollutants and produce hydrogen-enriched gases. The simulated o-cresol wastewater was gasified at 440-650 degrees C and 27.6 MPa in a continuous Inconel 625 reactor with the residence time of 0.42-1.25 min. The influence of the reaction temperature, residence time, pressure, catalyst, oxidant and the pollutant concentration on the gasification efficiency was investigated. Higher temperature and longer residence time enhanced the o-cresol gasification. The TOC removal rate and hydrogen gasification rate were 90.6% and 194.6%, respectively, at the temperature of 650 degrees C and the residence time of 0.83 min. The product gas was mainly composed of H2, CO2, CH4 and CO, among which the total molar percentage of H2 and CH4 was higher than 50%. The gasification efficiency decreased with the pollutant concentration increasing. Both the catalyst and oxidant could accelerate the hydrocarbon gasification at a lower reaction temperature, in which the catalyst promoted H2 production and the oxidant enhanced CO2 generation. The intermediates of liquid effluents were analyzed and phenol was found to be the main composition. The results indicate that the supercritical gasification is a promising way for the treatment of hazardous organic wastewater.

Bioelectric Energy Sources↗

PubMed2006

Fast de novo peptide sequencing and spectral alignment via tree decomposition.

De novo sequencing and spectral alignment are computationally important for the prediction of new protein peptides via tandem mass spectrometry (MS/MS). Both approaches are established upon the problem of finding the longest antisymmetric path on formulated graphs. The problem is of high computational complexity and the prediction accuracy is compromised when given spectra involve noisy data, missing mass peaks, or post translational modifications (PTMs) and mutations. This paper introduces a graphical mechanism to describe relationships among mass peaks that, through graph tree decomposition, yields linear and quadratic time algorithms for optimal de novo sequencing and spectral alignment respectively. Our test results show that, in addition to high efficiency, the new algorithms can achieve desired prediction accuracy on spectra containing noisy peaks and PTMs while allowing the presence of both b-ions and y-ions.

Algorithms↗

PubMed2006

A point-process model for rapid identification of post-translational modifications.

Post-translational modifications (PTMs) are very important to biological function, and yet are notoriously difficult to detect and identify, especially in a high-throughput manner. Most of the existing approaches rely on exhaustive searches which are highly time consuming and thus are currently limited to handling of a few types of PTMs. In this paper, we present a point-process model that aims to find the optimal mass shifts to maximize the spectra alignment between an experimental MS/MS spectrum and a candidate theoretical spectrum, through cross-correlation calculation, yields a rapid search for all types of PTMs in a blind mode, i.e., without giving the types of the searching PTMs in advance. The test results show that our new approach's performance is comparable to or better than the other blind search methods, but is more efficient computationally and simpler in its concept.

Algorithms↗

PubMed2005

Structural genomics analysis of alternative splicing and application to isoform structure modeling.

Alternative splicing is a sophisticated nuclear process that regulates gene expression. It represents an important mechanism for enhancing the functional diversity of proteins. Our current knowledge of alternatively spliced variants is derived mainly from mRNA transcripts, and very little is known about their protein tertiary structures. We carried out a large-scale analysis of known alternatively spliced variants at both protein sequence and structure levels and have shown that threading is, in general, a viable approach for modeling structures of alternatively spliced variants. An examination of alternative splicing at the protein sequence level revealed that the size of splicing events follows the power law distribution and the majority of splicing isoforms harbor only one or two alternations. We examined alternative splicing in the context of protein 3D structures and found that the boundaries of alternative splicing events generally happen in coil regions of secondary structures and exposed residues and the majority of the sequences involved in splicing are located on the surface of proteins. In light of these findings, we then proceeded to demonstrate that threading represents a useful tool for structure prediction of alternative splicing isoforms and addressed the fold stability issue of threading-based structure prediction by molecular dynamics simulation. Our analysis and the insights gained have helped to establish a viable method for structure prediction of alternatively spliced isoforms at the genome scale.

Alternative Splicing↗

PubMed2005

Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential.

Computational evaluation of protein-DNA interaction is important for the identification of DNA-binding sites and genome annotation. It could validate the predicted binding motifs by sequence-based approaches through the calculation of the binding affinity between a protein and DNA. Such an evaluation should take into account structural information to deal with the complicated effects from DNA structural deformation, distance-dependent multi-body interactions and solvation contributions. In this paper, we present a knowledge-based potential built on interactions between protein residues and DNA tri-nucleotides. The potential, which explicitly considers the distance-dependent two-body, three-body and four-body interactions between protein residues and DNA nucleotides, has been optimized in terms of a Z-score. We have applied this knowledge-based potential to evaluate the binding affinities of zinc-finger protein-DNA complexes. The predicted binding affinities are in good agreement with the experimental data (with a correlation coefficient of 0.950). On a larger test set containing 48 protein-DNA complexes with known experimental binding free energies, our potential has achieved a high correlation coefficient of 0.800, when compared with the experimental data. We have also used this potential to identify binding motifs in DNA sequences of transcription factors (TF). The TFs in 79.4% of the known TF-DNA complexes have accurately found their native binding sequences from a large pool of DNA sequences. When tested in a genome-scale search for TF-binding motifs of the cyclic AMP regulatory protein (CRP) of Escherichia coli, this potential ranks all known binding motifs of CRP in the top 15% of all candidate sequences.

Base Sequence↗

PubMed2005

Step-wise specification of retinal stem cells during normal embryogenesis.

The specification of embryonic cells to produce the retina begins at early embryonic stages as a multi-step process that gradually restricts fate potentials. First, a subset of embryonic cells becomes competent to form retina by their lack of expression of endo-mesoderm-specifying genes. From these cells, a more restricted subset is biased to form retina by virtue of their close proximity to sources of bone morphogenetic protein antagonists during neural induction. During gastrulation, the definitive RSCs (retinal stem cells) are specified as the eye field by interactions with underlying mesoderm and the expression of a network of retina-specifying genes. As the eye field is transformed into the optic vesicle and optic cup, a heterogeneous population of RPCs (retinal progenitor cells) forms to give rise to the different domains of the retina: the optic stalk, retinal pigmented epithelium and neural retina. Further diversity of RPCs appears to occur under the influences of cell-cell interactions, cytokines and combinations of regulatory genes, leading to the differentiation of a multitude of different retinal cell types. This review examines what is known about each sequential step in retinal specification during normal vertebrate development, and how that knowledge will be important to understand how RSCs might be manipulated for regenerative therapies to treat retinal diseases.

Animals↗

PubMed2005

[Expression of metabotropic glutamate receptor 1alpha in different brain areas of the kindled epilepsia models of rats by Coriaria lactone].

OBJECTIVE: To detect the expression of Metabotropic Glutamate Receptor 1alpha (MGLUR1alpha) in the different brain areas of the kindled epilepsia models of rats by Coriaria Lactone (CL). METHODS: Thirty male SD rats were divided into 3 groups and were given intramuscular injections of 0.75, 1.0 and 1.25 ml/kg Coriaria Lactone respectively. 5 rats in the control group were given intramuscular injection of 1.0 ml/kg saline. After the kindling models were completed, the EcoG of all groups were recorded with the multi-electrophysiology recorder to view whether the EcoG of kindled rats accord with their seizures and to know whether there are differencees in EcoG among the kindled, non-kindled and control groups. The coronary sections of brain tissue were HE stained and MGLUR1alpha immunohistochemistry stained, and were observed under light microscope. RESULTS: The kindled rats had all grade (Simialowski scale) seizures after CL injection and their seizures accorded with their EcoG features. The MGLUR1alpha expression of kindled rats in hippocampus and temporal cortex outside hippocampus was stronger than that of non-kindled and control rats (P < 0.05); the strong expression was noted to be of no obvious difference between neuron and glia. CONCLUSION: The MGLUR1alpha expression of kindled rats in hippocampus and temporal cortex outside hippocampus is stronger than that of non-kindled and control. It is possible that MGLUR1alpha participates in epileptic seizures.

Animals↗

PubMed2004

A graph-theoretic approach for the separation of b and y ions in tandem mass spectra.

MOTIVATION: Ion-type identification is a fundamental problem in computational proteomics. Methods for accurate identification of ion types provide the basis for many mass spectrometry data interpretation problems, including (a) de novo sequencing, (b) identification of post-translational modifications and mutations and (c) validation of database search results. RESULTS: Here, we present a novel graph-theoretic approach for solving the problem of separating b ions from y ions in a set of tandem mass spectra. We represent each spectral peak as a node and consider two types of edges: type-1 edge connecting two peaks probably of the same ion types and type-2 edge connecting two peaks probably of different ion types. The problem of ion-separation is formulated and solved as a graph partition problem, which is to partition the graph into three subgraphs, representing b, y and others ions, respectively, through maximizing the total weight of type-1 edges while minimizing the total weight of type-2 edges within each partitioned subgraph. We have developed a dynamic programming algorithm for rigorously solving this graph partition problem and implemented it as a computer program PRIME (PaRtition of Ion types in tandem Mass spEctra). The tests on a large amount of simulated mass spectra and 19 sets of high-quality experimental Fourier transform ion cyclotron resonance tandem mass spectra indicate that an accuracy level of approximately 90% for the separation of b and y ions was achieved. AVAILABILITY: The executable code of PRIME is available upon request. CONTACT: xyn@bmb.uga.edu.

Algorithms↗

PubMed2004

Separation of ion types in tandem mass spectrometry data interpretation -- a graph-theoretic approach.

Mass spectrometry is one of the most popular analytical techniques for identification of individual proteins in a protein mixture, one of the basic problems in proteomics. It identifies a protein through identifying its unique mass spectral pattern. While the problem is theoretically solvable, it remains a challenging problem computationally. One of the key challenges comes from the difficulty in distinguishing the N- and C-terminus ions, mostly b- and y-ions respectively. In this paper, we present a graph algorithm for solving the problem of separating bfrom y-ions in a set of mass spectra. We represent each spectral peak as a node and consider two types of edges: a type-1 edge connects two peaks possibly of the same ion types and a type-2 edge connects two peaks possibly of different ion types, predicted based on local information. The ion-separation problem is then formulated and solved as a graph partition problem, which is to partition the graph into three subgraphs, namely b-, y-ions and others respectively, so to maximize the total weight of type-1 edges while minimizing the total weight of type-2 edges within each subgraph. We have developed a dynamic programming algorithm for rigorously solving this graph partition problem and implemented it as a computer program PRIME. We have tested PRIME on 18 data sets of high accurate FT-ICR tandem mass spectra and found that it achieved ~90% accuracy for separation of b- and y- ions.

Algorithms↗

PubMed2003

Theoretical studies on competitive binding of caldesmon and myosin S1 to actin: prediction of apparent cooperativity in equilibrium and slow-down in kinetics of S1 binding by caldesmon.

Several laboratories have reported cooperative binding of S1 to actin in the presence of caldesmon. This cooperative binding has been interpreted with a model similar to that proposed for the binding of S1 to regulated actins in which the binding affinity of S1 is controlled by the position of the tropomyosin filaments. In a recent paper [Sen, A., Chen, Y., Yan, B., and Chalovich, J. M. (2001) Biochemistry 40, 5757-64], we showed qualitatively that S1 binding resulted in rapid dissociation of caldesmon from actin or actin-tropomyosin. This suggests that the cooperativity observed in the case of caldesmon is not due to a conformational change in actin-caldesmon but to the displacement of caldesmon. We show in this paper that the pure competitive binding model, in which both S1 and caldesmon are competing for the same binding sites on actin, can simulate quantitatively the effect of caldesmon on both the equilibrium and the kinetics of S1 binding to actin. This model successfully predicts an apparent cooperativity for the binding of S1 to actin-caldesmon without the need to assume multiple actin-caldesmon structures and produces a decreased rate of S1 binding to actin in the presence of caldesmon. This suggests that the inhibitory action of caldesmon on the actin-activated ATPase activity of myosin in solution and on the generation of active force in a contracting muscle may be simply due to the blocking of myosin binding sites on actin by caldesmon.

Actins↗

PubMed2003

A BAC-based physical map of the chicken genome.

A genome-wide physical map constructed with bacterial artificial chromosomes (BACs) is an essential component in linking phenotypic traits to the responsible genetic variation in the genomes of plants and animals. We have constructed a physical map of the chicken genome from 57,091 BACs (7.9-fold haploid genome coverage) by restriction fingerprint analysis using high-resolution polyacrylamide gel electrophoresis. The physical map consists of 2331 overlapping BAC contigs and is estimated to span 1510 Mb in physical length. BAC contigs were verified manually and by screening the BACs with 367 DNA markers. A total of 361 of the contigs have been anchored to the existing chicken genetic map. This map represents the first genome-wide, BAC-based physical map of the chicken genome. It provides a powerful platform for many areas of chicken genomics, including targeted marker development, fine mapping of genes and QTL alleles, positional cloning, analysis of avian genome organization and evolution, chicken-mammalian comparative genomics, and large-scale genome sequencing.

Animals↗