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author:("Zhang, jiayin")
1.  Prediction of disease-related genes based on weighted tissue-specific networks by using DNA methylation 
BMC Medical Genomics  2014;7(Suppl 2):S4.
Background
Predicting disease-related genes is one of the most important tasks in bioinformatics and systems biology. With the advances in high-throughput techniques, a large number of protein-protein interactions are available, which make it possible to identify disease-related genes at the network level. However, network-based identification of disease-related genes is still a challenge as the considerable false-positives are still existed in the current available protein interaction networks (PIN).
Results
Considering the fact that the majority of genetic disorders tend to manifest only in a single or a few tissues, we constructed tissue-specific networks (TSN) by integrating PIN and tissue-specific data. We further weighed the constructed tissue-specific network (WTSN) by using DNA methylation as it plays an irreplaceable role in the development of complex diseases. A PageRank-based method was developed to identify disease-related genes from the constructed networks. To validate the effectiveness of the proposed method, we constructed PIN, weighted PIN (WPIN), TSN, WTSN for colon cancer and leukemia, respectively. The experimental results on colon cancer and leukemia show that the combination of tissue-specific data and DNA methylation can help to identify disease-related genes more accurately. Moreover, the PageRank-based method was effective to predict disease-related genes on the case studies of colon cancer and leukemia.
Conclusions
Tissue-specific data and DNA methylation are two important factors to the study of human diseases. The same method implemented on the WTSN can achieve better results compared to those being implemented on original PIN, WPIN, or TSN. The PageRank-based method outperforms degree centrality-based method for identifying disease-related genes from WTSN.
doi:10.1186/1755-8794-7-S2-S4
PMCID: PMC4243158  PMID: 25350763
2.  Genetic polymorphisms of VIP variants in the Tajik ethnic group of northwest China 
BMC Genetics  2014;15(1):102.
Background
Individual response to medications varies significantly among different populations, and great progress in understanding the molecular basis of drug action has been made in the past 50 years. The field of pharmacogenomics seeks to elucidate inherited differences in drug disposition and effects. While we know that different populations and ethnic groups are genetically heterogeneous, we have not found any pharmacogenomics information regarding minority groups, such as the Tajik ethnic group in northwest China.
Results
We genotyped 85 Very Important Pharmacogene (VIP) variants selected from PharmGKB in 100 unrelated, healthy Tajiks from the Xinjiang Uygur Autonomous Region and compared our data with HapMap data from four major populations around the world: Han Chinese (CHB), Japanese in Tokyo (JPT), Utah Residents with Northern and Western European Ancestry (CEU), and Yorubia in Ibadan, Nigeria (YRI). We found that Tajiks differed from CHB, JPT and YRI in 30, 32, and 32 of the selected VIP genotypes respectively (p < 0.005), while differences between Tajiks and CEU were found in only 6 of the genotypes (p < 0.005). Haplotype analysis also demonstrated differences between the Tajiks and the other four populations.
Conclusion
Our results contribute to the pharmacogenomics database of the Tajik ethnic group and provide a theoretical basis for safer drug administration that may be useful for diagnosing and treating disease in this population.
Electronic supplementary material
The online version of this article (doi:10.1186/s12863-014-0102-y) contains supplementary material, which is available to authorized users.
doi:10.1186/s12863-014-0102-y
PMCID: PMC4189671  PMID: 25266489
Pharmacogenomics; Genetic polymorphism; Haplotype; Tajik; Ethnic difference
3.  Genome Sequence of a Salmonella Phage Used To Control Salmonella Transmission in Swine 
Genome Announcements  2014;2(5):e00521-14.
Salmonella shedding in swine often increases in response to transportation and lairage. We previously demonstrated that such increases can be limited by directly feeding microencapsulated Salmonella bacteriophages. Here we present the genome sequence of vB_SalM_SJ_3, a broader spectrum Viuna-like Salmonella phage used in those studies.
doi:10.1128/genomeA.00521-14
PMCID: PMC4161739  PMID: 25212610
4.  Genetic association between selected cytokine genes and glioblastoma in the Han Chinese population 
BMC Cancer  2013;13:236.
Background
Glioblastoma (GBM) is the most malignant brain tumor. Many abnormal secretion and expression of cytokines have been found in GBM, initially speculated that the occurrence of GBM may be involved in these abnormal secretion of cytokines. This study aims to detect the association of cytokine genes with GBM.
Methods
We selected seven tag single nucleotide polymorphisms (tSNPs) in six cytokine genes, which previously reported to be associated with brain tumors, and analyzed their association with GBM in a Han Chinese population using χ2 test and genetic model analysis.
Results
We found two risk tSNPs and one protective tSNP. By χ2 test, the rs1801275 in IL-4R showed an increased risk of GBM. In the genetic model analysis, the genotype “TC” of rs20541 in IL-13 gene showed an increased risk of GBM in over-dominant model (OR = 2.00; 95% CI, 1.13-3.54, p = 0.015); the genotype “CT” of rs1800871 in the IL-10 gene showed a decrease risk in the over-dominant model (OR = 0.57; 95% CI, 0.33 – 0.97; p = 0.037). The genotype “AG” of rs1801275 in the IL-4R gene showed an increase risk in over-dominant model (OR = 2.29; 95% CI, 1.20 - 4.35; p = 0.0081) We further analyzed whether the six cytokine genes have a different effect on the disease in gender specific population, and found that the allele “G” of rs2243248 in the IL-4 gene showed a decrease risk of GBM in female (OR = 0.35, 95% CI, 0.13 - 0.94, p = 0.0032), but the allele “T” showed a decrease risk in male (OR = 0.30, 95% CI, 0.17 - 0.53, p = 0.0032).
Conclusions
Our findings, combined with previously reported results, suggest that cytokine genes have potential role in GBM development, which may be useful to early prognostics for GBM in the Han Chinese population.
doi:10.1186/1471-2407-13-236
PMCID: PMC3655821  PMID: 23663500
Cytokine gene; Glioblastoma (GBM); Tag single nucleotide polymorphism (tSNP); Case–control study
5.  Visual Map Development Depends On The Temporal Pattern of Binocular Activity in Mice 
Nature Neuroscience  2011;15(2):298-307.
Binocular competition is thought to drive eye-specific segregation in the developing visual system, potentially through Hebbian synaptic learning rules that are sensitive to correlations in afferent activity. Altering retinal activity can disrupt eye-specific segregation, but little is known about the temporal features of binocular activity that modulate visual map development. We used optogenetic techniques to directly manipulate retinal activity in vivo and identified a critical period before eye opening in mice when specific binocular features of retinal activity drive visual map development. Synchronous activation of both eyes disrupted segregation, whereas asynchronous stimulation enhanced segregation. The optogenetic stimulus applied was spatially homogenous, and accordingly retinotopy of ipsilateral projections was dramatically perturbed, but contralateral retinotopy was unaffected or even improved. These results provide direct evidence that the synchrony and precise temporal pattern of binocular retinal activity during a critical period in development regulates eye-specific segregation and retinotopy in the developing visual system.
doi:10.1038/nn.3007
PMCID: PMC3267873  PMID: 22179110
Retinal Waves; Superior Colliculus; Visual Development; Retinotopy; Eye Segregation; Lateral Geniculate Nucleus; Critical Period
6.  Visualization and Manipulation of Neural Activity in the Developing Vertebrate Nervous System 
Neural activity during vertebrate development has been unambiguously shown to play a critical role in sculpting circuit formation and function. Patterned neural activity in various parts of the developing nervous system is thought to modulate neurite outgrowth, axon targeting, and synapse refinement. The nature and role of patterned neural activity during development has been classically studied with in vitro preparations using pharmacological manipulations. In this review we discuss newly available and developing molecular–genetic tools for the visualization and manipulation of neural activity patterns specifically during development.
doi:10.3389/fnmol.2011.00043
PMCID: PMC3219918  PMID: 22121343
optogenetics; development; neuron; circuit; vision; imaging
7.  Integrated device for optical stimulation and spatiotemporal electrical recording of neural activity in light-sensitized brain tissue 
Journal of neural engineering  2009;6(5):055007.
Neural stimulation with high spatial and temporal precision is desirable both for studying the real-time dynamics of neural networks and for prospective clinical treatment of neurological diseases. Optical stimulation of genetically targeted neurons expressing the light sensitive channel protein Channelrhodopsin (ChR2) has recently been reported as a means for millisecond temporal control of neuronal spiking activities with cell-type selectivity. This offers the prospect of enabling local delivery of optical stimulation and the simultaneous monitoring of the neural activity by electrophysiological means, both in the vicinity of and distant to the stimulation site. We report here a novel dual-modality hybrid device, which consists of a tapered coaxial optical waveguide (‘optrode’) integrated into a 100 element intra-cortical multi-electrode recording array. We first demonstrate the dual optical delivery and electrical recording capability of the single optrode in in vitro preparations of mouse retina, photo-stimulating the native retinal photoreceptors while recording light-responsive activities from ganglion cells. The dual-modality array device was then used in ChR2 transfected mouse brain slices. Specifically, epileptiform events were reliably optically triggered by the optrode and their spatiotemporal patterns were simultaneously recorded by the multi-electrode array.
doi:10.1088/1741-2560/6/5/055007
PMCID: PMC2921864  PMID: 19721185
8.  Phage Therapy To Reduce Preprocessing Salmonella Infections in Market-Weight Swine▿  
Contamination of meat products with food-borne pathogens usually results from the carcass coming in contact with the feces of an infected animal during processing. In the case of Salmonella, pigs can become colonized with the organism during transport and lairage from contaminated trailers and holding pens, resulting in increased pathogen shedding just prior to processing. Increased shedding, in turn, amplifies the likelihood of carcass contamination by magnifying the amount of bacteria that enters the processing facility. We conducted a series of experiments to test whether phage therapy could limit Salmonella infections at this crucial period. In a preliminary experiment done with small pigs (3 to 4 weeks old; 30 to 40 lb), administration of an anti-Salmonella phage cocktail at the time of inoculation with Salmonella enterica serovar Typhimurium reduced Salmonella colonization by 99.0 to 99.9% (2- to 3-log reduction) in the tonsils, ileum, and cecum. To test the efficacy of phage therapy in a production-like setting, we inoculated four market-weight pigs (in three replicates) with Salmonella enterica serovar Typhimurium and allowed the challenged pigs to contaminate a holding pen for 48 h. Sixteen naïve pigs were randomly split into two groups which received either the anti-Salmonella phage cocktail or a mock treatment. Both groups of pigs were comingled with the challenged pigs in the contaminated pen. Treatment with the anti-Salmonella phage cocktail significantly reduced cecal Salmonella concentrations (95%; P < 0.05) while also reducing (numerically) ileal Salmonella concentrations (90%; P = 0.06). Additional in vitro studies showed that the phage cocktail was also lytic against several non-Typhimurium serovars.
doi:10.1128/AEM.00785-09
PMCID: PMC2798657  PMID: 19854929

Results 1-8 (8)