Biomedical subjects

Ping Song

Publications and source records attributed to Ping Song.

At least 19 recordsLinked to original sources

PubMed2024

Integrated bioinformatics analysis and experimental validation reveal the relationship between ALOX5AP and the prognosis and immune microenvironment in glioma.

BACKGROUND: Treatment of gliomas, the most prevalent primary malignant neoplasm of the central nervous system, is challenging. Arachidonate 5-lipoxygenase activating protein (ALOX5AP) is crucial for converting arachidonic acid into leukotrienes and is associated with poor prognosis in multiple cancers. Nevertheless, its relationship with the prognosis and the immune microenvironment of gliomas remains incompletely understood. METHODS: The differential expression of ALOX5AP was evaluated based on public Databases. Kaplan-Meier, multivariate Cox proportional hazards regression analysis, time-dependent receiver operating characteristic, and nomogram were used to estimate the prognostic value of ALOX5AP. The relationship between ALOX5AP and immune infiltration was calculated using ESTIMATE and CIBERSORT algorithms. Relationships between ALOX5AP and human leukocyte antigen molecules, immune checkpoints, tumor mutation burden, TIDE score, and immunophenoscore were calculated to evaluate glioma immunotherapy response. Single gene GSEA and co-expression network-based GO and KEGG enrichment analysis were performed to explore the potential function of ALOX5AP. ALOX5AP expression was verified using multiplex immunofluorescence staining and its prognostic effects were confirmed using a glioma tissue microarray. RESULT: ALOX5AP was highly expressed in gliomas, and the expression level was related to World Health Organization (WHO) grade, age, sex, IDH mutation status, 1p19q co-deletion status, MGMTp methylation status, and poor prognosis. Single-cell RNA sequencing showed that ALOX5AP was expressed in macrophages, monocytes, and T cells but not in tumor cells. ALOX5AP expression positively correlated with M2 macrophage infiltration and poor immunotherapy response. Immunofluorescence staining demonstrated that ALOX5AP was upregulated in WHO higher-grade gliomas, localizing to M2 macrophages. Glioma tissue microarray confirmed the adverse effect of ALOX5AP in the prognosis of glioma. CONCLUSION: ALOX5AP is highly expressed in M2 macrophages and may act as a potential biomarker for predicting prognosis and immunotherapy response in patients with glioma.

Humans↗

PubMed2021

Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology.

Circulating tumor DNA (ctDNA) sequencing is being rapidly adopted in precision oncology, but the accuracy, sensitivity and reproducibility of ctDNA assays is poorly understood. Here we report the findings of a multi-site, cross-platform evaluation of the analytical performance of five industry-leading ctDNA assays. We evaluated each stage of the ctDNA sequencing workflow with simulations, synthetic DNA spike-in experiments and proficiency testing on standardized, cell-line-derived reference samples. Above 0.5% variant allele frequency, ctDNA mutations were detected with high sensitivity, precision and reproducibility by all five assays, whereas, below this limit, detection became unreliable and varied widely between assays, especially when input material was limited. Missed mutations (false negatives) were more common than erroneous candidates (false positives), indicating that the reliable sampling of rare ctDNA fragments is the key challenge for ctDNA assays. This comprehensive evaluation of the analytical performance of ctDNA assays serves to inform best practice guidelines and provides a resource for precision oncology.

Circulating Tumor DNA↗

PubMed2006

Two novel transcripts encoding two Ankyrin repeat containing proteins have preponderant expression during the mouse spermatogenesis.

The clone 4921537P18 expressed preponderantly in mouse testis was identified by screening the Riken cDNA database, and two new full-length isoforms of this clone, which were named gsarp1 (Gonad Specific Ankyrin Repeat (ANK) Protein 1) and gsarp2, were found and isolated from mouse testis in the course of the research. Both of the GSARP1 and GSARP2 contain an ANK region circular composed by seven ANKs, and their structural feature is very similar to that of the IkappaB family proteins, while IkappaB proteins associate with the transcription factor NF-kappaB via their ANKs in the NF-kappaB pathway. We investigated the expression pattern at the mRNA level by Reverse transcription PCR. The gsarp1 has high expression level in mouse testis, while has low expression level in the ovary, and the gsarp2 is only expressed in mouse testis. The gsarp1 and gsarp2 begin to be detected at the early and later pachytene stage of meiosis separately, while both have high-expression level at the stage of MI and MII. The result of in situ hybridization reveals that the gsarp1 is primarily expressed in spermatocytes, while gsarp2 is expressed in spermatocytes and spermatids. In view of the structural feature and expression pattern of the GSARP1 and GSARP2, we speculate that they may play a certain role in a signal pathway of meiosis.

Amino Acid Sequence↗

PubMed2006

A real-time quantitative PCR detection method specific to widestrike transgenic cotton (event 281-24-236/3006-210-23).

In compliance with global regulations on transgenic crops, a real-time quantitative PCR method specific to Widestrike transgenic cotton (event 281-24-236/3006-210-23, OECD Unique Identifier DAS-24236-5/DAS-21023-5) was established on the basis of the DNA sequences in the junction between the transgene insert and cotton genome. The optimized method consists of a DNA extraction method for cotton seeds and three PCR systems corresponding to a cotton-specific endogenous reference DNA sequence SAH7 (Sinapis Arabidopsis Homolog 7) and specific detection of event 281-24-236 and event 3006-210-23. The method performance including specificity, sensitivity, accuracy, and precision was determined at a dynamic range of Widestrike DNA levels from 0.04% to 5.0%. The limits of detection (LOD) and quantification (LOQ) were < or =0.04% and < or =0.09%, respectively, at 100 ng of DNA sample per reaction. The quantification results using either the event 281-24-236 or 3006-210-23 system were consistent, and the relative deviation from the expected (true) value was in the range of +/-25%. The robustness of the method was demonstrated by a series of tests with deviations from the optimized assay parameters such as annealing temperature, extension time, PCR instrument, interlaboratory transferability, etc. All the measurements from these tests met the criteria set by EU JRC-CRL (European Commission Joint Research Centre-Community Reference Lab). This real-time quantitative PCR method is accurate and robust, and is recommended as a global benchmark method for the detection and quantification of Widestrike cotton. The method including description, protocol, and performance results is available on the JRC-CRL website (http://gmo-crl.jrc.it/statusofdoss.htm).

DNA, Plant↗

PubMed2006

Modulation of Kv3.1b potassium channel phosphorylation in auditory neurons by conventional and novel protein kinase C isozymes.

In fast-spiking neurons such as those in the medial nucleus of the trapezoid body (MNTB) in the auditory brainstem, Kv3.1 potassium channels are required for high frequency firing. The Kv3.1b splice variant of this channel predominates in the mature nervous system and is a substrate for phosphorylation by protein kinase C (PKC) at Ser-503. In resting neurons, basal phosphorylation at this site decreases Kv3.1 current, reducing neuronal ability to follow high frequency stimulation. We used a phospho-specific antibody to determine which PKC isozymes control serine 503 phosphorylation in Kv3.1b-tranfected cells and in auditory neurons in brainstem slices. By using isozyme-specific inhibitors, we found that the novel PKC-delta isozyme, together with the novel PKC-epsilon and conventional PKCs, contributed to the basal phosphorylation of Kv3.1b in MNTB neurons. In contrast, only PKC-epsilon and conventional PKCs mediate increases in phosphorylation produced by pharmacological activation of PKC in MNTB neurons or by metabotropic glutamate receptor activation in Kv3.1/mGluR1-cotransfected cells. We also measured the time course of dephosphorylation and recovery of basal phosphorylation of Kv3.1b following brief high frequency electrical stimulation of the trapezoid body, and we determined that the recovery process is mediated by both novel PKC-delta and PKC-epsilon isozymes and by conventional PKCs. The association between Kv3.1b and PKC isozymes was confirmed by reciprocal coimmunoprecipitation of Kv3.1b with multiple PKC isozymes. Our results suggest that the Kv3.1b channel is regulated by both conventional and novel PKC isozymes and that novel PKC-delta contributes specifically to the maintenance of basal phosphorylation in auditory neurons.

Animals↗

PubMed2006

Zebrafish z-otu, a novel Otu and Tudor domain-containing gene, is expressed in early stages of oogenesis and embryogenesis.

Several studies have suggested that Otu domain had de-ubiquitinating activity and Tudor domain was important for the formation of germ cells. Here, we reported a novel zebrafish ovary-specific gene containing Otu and Tudor domain, z-otu, which was expressed at stages I-III oocytes and embryonic stages from zygotes to early blastula during embryonic cells maintained their totipotency. Therefore, z-otu might link the ubiquitin signaling pathway to early oogenesis and maintaining the totipotency of embryonic cell.

Amino Acid Sequence↗

PubMed2006

FoxG1 haploinsufficiency results in impaired neurogenesis in the postnatal hippocampus and contextual memory deficits.

FoxG1 (formerly BF-1) encodes a transcription factor that regulates neurogenesis in the embryonic telencephalon. The current study suggests that FoxG1 also regulates neurogenesis in the postnatal hippocampus. FoxG1 continues to be strongly expressed in areas of known postnatal neurogenesis, including the subventricular zone of the lateral ventricle and the dentate gyrus (DG) of the hippocampus. Remarkably, FoxG1+/- mice have a 60% decrease in the total number of hippocampal dentate granule cells that is related to a loss of DG neurogenesis. Comparison of acute and chronic BrdU labeling, and PSA-NCAM staining suggests that the stage at which this loss of neurogenesis occurs progresses with age. Juvenile mice FoxG1+/- primarily show failed apparent survival of postnatally born DG neurons, whereas adult FoxG1+/- mice also show impairment of proliferation and initial DG neuron differentiation. Consistent with this process predominantly affecting postnatal hippocampal neurogenesis, BrdU pulses at embryonic days 16, 17, and 18 labels a higher percentage of DG cells in 6-week-old FoxG1+/- mice than in littermate controls. In contrast to the marked effect of FoxG1 haploinsufficiency on postnatal hippocampal neurogenesis, postnatal neurogenesis of olfactory bulb interneurons is grossly unaffected. Behaviorally, FoxG1+/- mice show hyperlocomotion and impaired habituation in the open field, and a severe deficit in contextual fear conditioning that are suggestive of impaired hippocampal function. Although mechanistic connections between FoxG1 haploinsufficiency and either failed postnatal DG neurogenesis or the behavioral deficits remain to be elucidated, these results present a new model system for impaired postnatal neurogenesis in the DG of adult mice.

Animals↗

PubMed2006

PSM2, a novel protein similar to MCAF2, is involved in the mouse embryonic and adult male gonad development.

By screening RIKEN database, we obtained a mouse ovary and uterus derived clone (RIKEN clone ID: 5031403I04). Multiple tissues expression analysis revealed that the clone was specifically expressed in ovary and to a higher extent in testis. It is expressed in early mouse embryo, especially in the embryonic gonad from 11.5 dpc (days post coitus). Furthermore, it is also expressed continuously from newborn testis to adult. Using testis sections in situ hybridization, we found the mRNA was localized to spermatogonia, round spermatids and mainly to spermatocytes. We cloned the cDNA from mouse testis. The gene consists of 10 exons spanning approximately 48 kb on mouse chromosome 16. The cDNA encodes a putative nuclear protein of 319 amino acids containing a coiled-coil motif. The deduced protein has high similarity with human MCAF2 (MBD1-containing chromatin-associated factor 2), so we termed it as PSM2 (protein similar to MCAF2) in this article. We therefore hypothesized that PSM2 might interact with some important partners by the conserved domain and be involved in the transcription modulation during gonad development.

Amino Acid Sequence↗

PubMed2006

Molecular cloning of a novel gene ZAhi-1 and its expression analysis during zebrafish gametogenesis.

Proto-oncogen Ahi-1 is closely related to a lot of human and mouse diseases. Ahi-1 mutation will lead to leukemia in mice and Joubert syndrome in human beings. We have cloned the full cDNA sequence of Ahi-1 homologous in zebrafish, and RT-PCR results of ZAhi-1 in different tissues reveal that ZAhi-1 expressed highest in the mature gonad. In situ hybridization results of zebrafish gonad show that ZAhi-1 only expressed in the early stages' gamete cells. RT-PCR analyses of mouse Ahi-1 in different stages of spermatogenesis have been done according to the published Ahi-1 sequence, and the findings reveal that Ahi-1 is expressed in gamete of pachytene stage. It can then be safely concluded that Ahi-1 might take place in the spermatocyte from the early pachytene stage to the late pachytene stage.

Amino Acid Sequence↗

PubMed2006

The identification and characterization of a testis-specific cDNA during spermatogenesis.

Using bioinformatics and experimental validation, we obtained a cDNA (named srsf) which was exclusively expressed in the mouse testes. RT-PCR analysis showed that srsf mRNA was not expressed in the gonad during the sex determination period or during embryogenesis. In developing mouse testis, srsf expression was first detected on post-natal day 10, reached its highest level on day 23, and then reduced to and remained at a moderate level throughout adulthood. In situ hybridization analysis demonstrated that srsf mRNA was expressed in pachytene spermatocytes and round spermatids in the testes. The predicted protein contains one RNA-binding domain (RBD) and a serine-arginine rich domain (RS), which are characterized by some splicing factors of SR family members. These findings indicate that srsf may play a role during spermatogenesis.

Amino Acid Sequence↗

PubMed2006

[Experimental study on mechanisms of lyophilized powder of fresh gekko Chinenis in inhibiting H22 hepatocarcinoma angiogenesis].

OBJECTIVE: To investigate the inhibitory effects and its mechanism of lyophilized powder of fresh Gekko Chinenis (GCLP) on H22 hepatocarcinoma growth and angiogenesis in vitro. METHODS: The transplant tumor model of H22 hepatocarcinoma in mice was established. Thirty mice were randomly divided into three groups, the cisplatin group, the GCLP group and the control group, they were treated respectively with intraperitoneal injection of cisplatin 1 mg/g, oral administration of GCLP in a dose of 1.2 g/kg, and equal volume of saline, the medication was given for 20 times totally. The anti-tumor activity was evaluated by tumor tissue weighing, the cell apoptotic rate was detected by TUNEL method, the micro-vessel density in tumor tissue was determined by Weidner method, the protein expression of vascular endothelin growth factor (VEGF) and basic fibroblast growth factor (bFGF) were detected by S-P immunohistochemistry. RESULTS: GCLP could obviously inhibit the hepatocarcinoma growth, induce tumor cell apoptosis, and reduce micro-vessel density in tumor tissue through down-regulating VEGF and bFGF protein expression. CONCLUSIONS: GCLP can effectively inhibit the growth of H22 hepatocarcinoma and angiogenesis. Its mechanism might be related to the down-regulation of the protein expression of VEGF and bFGF.

Angiogenesis Inhibitors↗

PubMed2006

[The study of ribosomal protein l15 cDNA sequences as a molecular marker in the teleostei phylogenetic analysis].

In this study, the full-length cDNAs of RPL15 (ribosomal protein L15) gene were cloned and sequenced from fifteen fishes of five orders under Teleostei. The complete ORF sequences were analyzed for phylogenetic reconstruction for the first time to evaluate the potential of RPL15 gene as a novel marker in resolving teleostean phylogenetic relationships. The resultant NJ, MP and ML trees with Anguilla japonica as the outgroup were generally resolved and largely congruent with the morphology-based tree though some incongruities were observed. The incongruities were then analyzed for some explanations. The results suggested that: (1) RPL15 gene was highly conserved during eukaryotic evolution; (2) RPL15 ORF might be a good phylogenetic marker for resolving teleostean relationships. It might be especially appropriate for the higher-level relationships (such as interordinal), and it was possibly suitable for lower-level relationships as well. The same can be true for other eukaryotes.

Animals↗

PubMed2006

[Determination of alpha-linolenic acid in perilla oil by reversed-phase high performance liquid chromatography coupled with evaporative light-scattering detector].

A method for the determination of alpha-linolenic acid in perilla oil was developed using the reversed-phase high performance liquid chromatography coupled with evaporative light-scattering detector (RP-HPLC-ELSD). The perilla oil was saponified by 0.5 mol/L KOH-CH3OH solution for 20 min in a 60 degrees C water bath, then acidified by 6 mol/L HCl and finally the dissociative fatty acids, including alpha-linolenic acid, was extracted by anhydrous ether. After the ether was blown out by nitrogen, the residuals were dissolved by 10 mL methanol. The calibration curve was found to be linear over the range of 6.2 - 45.4 microg (r = 0.997 3, n = 5) and the detection limit was 0.11 microg (S/N = 3). The average recovery was 102% and their relative standard deviation (RSD) was 6.3% (n = 5). The content of alpha-linolenic acid in the determined perilla oil was 6.79% which is consistent with the previous report.

Chromatography, High Pressure Liquid↗

PubMed2006

[Mechanism of IL-6 on acrosome reaction in human sperm].

OBJECTIVE: To explore the mechanism of interleukin-6 (IL-6) on acrosome reaction (AR) in human sperm. METHODS: Sperm acrosin activity was measured by BAEE/ADH and AR evaluated by FITC-PSA. RESULTS: IL-6 could induce the activity of acrosin and superoxide dismutase (SOD) and enhance AR in human sperm. AR was not induced by extracellular Ca2+, and IL-6-induced AR did not occur in Ca2(+)-free medium. Calphostin C, one inhibitor of the protein kinase C (PKC), could block IL-6-induced AR in human sperm. CONCLUSION: IL-6 could induce AR by stimulating the activity of acrosin and SOD in human sperm, which also involves the activation of PKC, and requires the presence of extracellular Ca2+.

Acrosin↗

PubMed2006

[Prevalence and risk factors of social anxiety disorder in high schools and universities in Chengdu].

OBJECTIVE: To explore the prevalence and risk factors of social anxiety disorder (SAD) in high schools and universities in Chengdu. METHODS: 2279 students in Chengdu sampled by optimum distributing delaminating grouping method were interviewed one-to-one by the trained psychiatrists according to SCID. Both the cooperated SAD patients (n=156) and the normal counterparts (NC, n=156) in the 2279 students completed Egma Minnen av Bardndosnauppforstran (EMBU), State-Trait Anxiety Inventory (STAI-Form Y), Fear of Negative Evaluation Scale (FNE) and Defense Style Questionnaire (DSQ). RESULTS: There were 179 SAD patients, 88 female ones and 91 male ones, in the 2279 students of the high schools and universities in Chengdu. Statistical analysis reveals that the SAD patients differ from the NC in seven aspects, i.e. growing circumstances (P = 0.049), family economical status(P = 0.000), family history of psychiatric disorder, scales of EMBU,STAI, FNE and DSQ. CONCLUSION: The total prevalence of SAD in the students of high schools and universities in Chengdu was 8.15%, the female prevalence 8.35%, and the male prevalence 7.62%. The possible risk factors were: growing up in the countryside, low family economic state, parental rearing pattern being deficient in emotional warmth, understanding, trust and encouragement but excessive in refuse, denial and overprotection, having anxiety trait, feeling fear of negative evaluation, more likely to use neurotic and immature defense mechanism while less likely to use mature defense mechanism, having positive family mental disorder history.

Adolescent↗

PubMed2005

The value of short amino acid sequence matches for prediction of protein allergenicity.

Typically, genetically engineered crops contain traits encoded by one or a few newly expressed proteins. The allergenicity assessment of newly expressed proteins is an important component in the safety evaluation of genetically engineered plants. One aspect of this assessment involves sequence searches that compare the amino acid sequence of the protein to all known allergens. Analyses are performed to determine the potential for immunologically based cross-reactivity where IgE directed against a known allergen could bind to the protein and elicit a clinical reaction in sensitized individuals. Bioinformatic searches are designed to detect global sequence similarity and short contiguous amino acid sequence identity. It has been suggested that potential allergen cross-reactivity may be predicted by identifying matches as short as six to eight contiguous amino acids between the protein of interest and a known allergen. A series of analyses were performed, and match probabilities were calculated for different size peptides to determine if there was a scientifically justified search window size that identified allergen sequence characteristics. Four probability modeling methods were tested: (1) a mock protein and a mock allergen database, (2) a mock protein and genuine allergen database, (3) a genuine allergen and genuine protein database, and (4) a genuine allergen and genuine protein database combined with a correction for repeating peptides. These analyses indicated that searches for short amino acid sequence matches of eight amino acids or fewer to identify proteins as potential cross-reactive allergens is a product of chance and adds little value to allergy assessments for newly expressed proteins.

Allergens↗

PubMed2005

Acoustic environment determines phosphorylation state of the Kv3.1 potassium channel in auditory neurons.

Sound localization by auditory brainstem nuclei relies on the detection of microsecond interaural differences in action potentials that encode sound volume and timing. Neurons in these nuclei express high amounts of the Kv3.1 potassium channel, which allows them to fire at high frequencies with short-duration action potentials. Using computational modeling, we show that high amounts of Kv3.1 current decrease the timing accuracy of action potentials but enable neurons to follow high-frequency stimuli. The Kv3.1b channel is regulated by protein kinase C (PKC), which decreases current amplitude. Here we show that in a quiet environment, Kv3.1b is basally phosphorylated in rat brainstem neurons but is rapidly dephosphorylated in response to high-frequency auditory or synaptic stimulation. Dephosphorylation of the channel produced an increase in Kv3.1 current, facilitating high-frequency spiking. Our results indicate that the intrinsic electrical properties of auditory neurons are rapidly modified to adjust to the ambient acoustic environment.

Acoustic Stimulation↗

PubMed2005

Cloning and characterization of full length of a novel zebrafish gene Zsrg abundantly expressed in the germline stem cells.

Using the digital differential display program of the National Center for Biotechnology Information, we identified a contig of expression sequence tags (ESTs) (Accession No. BM316936), which came from zebrafish ovary and testis libraries. The full-length cDNA of this transcript was cloned and further confirmed by polymerase chain reaction and sequencing. The full-length cDNA of the novel gene is 807bp and encodes a novel protein of 187 amino acids, which shares no significant homology with any other known proteins. Characterization of genomic sequences of the gene revealed that it spans 6kb on the linkage group 3 and is composed of five exons and four introns. RT-PCR analysis showed that it was expressed in mature oocytes and one-cell stage, and persisted until 24h of development. RT-PCR also revealed that it is expressed in gonad and kidney, with the highest level of expression in the testis. The expression sites of the novel gene in adult gonad were further localized by in situ hybridization to oogonia and growing oocytes in ovary and to spermatogonia, spermatocytes but not to spermatids in testis. Based on its abundance in testis and the germline stem cell-spermatogonia and oogonia, we hypothesize that it may function as a testicular development and gametogenesis related gene that plays important roles in spermatogenesis, and named it Zsrg (zebrafish testis spermatogenesis related gene, Zsrg).

Amino Acid Sequence↗