An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases

<p>Abstract</p> <p>Background</p> <p>Studies on the relationship between disease and genetic variations such as single nucleotide polymorphisms (SNPs) are important. Genetic variations can cause disease by influencing important biological regulation processes. Despite the needs for analyzing SNP and disease correlation, most existing databases provide information only on functional variants at specific locations on the genome, or deal with only a few genes associated with disease. There is no combined resource to widely support gene-, SNP-, and disease-related information, and to capture relationships among such data. Therefore, we developed an integrated database-pipeline system for studying SNPs and diseases.</p> <p>Results</p> <p>To implement the pipeline system for the integrated database, we first unified complicated and redundant disease terms and gene names using the Unified Medical Language System (UMLS) for classification and noun modification, and the HUGO Gene Nomenclature Committee (HGNC) and NCBI gene databases. Next, we collected and integrated representative databases for three categories of information. For genes and proteins, we examined the NCBI mRNA, UniProt, UCSC Table Track and MitoDat databases. For genetic variants we used the dbSNP, JSNP, ALFRED, and HGVbase databases. For disease, we employed OMIM, GAD, and HGMD databases. The database-pipeline system provides a disease thesaurus, including genes and SNPs associated with disease. The search results for these categories are available on the web page <url>http://diseasome.kobic.re.kr/</url>, and a genome browser is also available to highlight findings, as well as to permit the convenient review of potentially deleterious SNPs among genes strongly associated with specific diseases and clinical phenotypes.</p> <p>Conclusion</p> <p>Our system is designed to capture the relationships between SNPs associated with disease and disease-causing genes. The integrated database-pipeline provides a list of candidate genes and SNP markers for evaluation in both epidemiological and molecular biological approaches to diseases-gene association studies. Furthermore, researchers then can decide semi-automatically the data set for association studies while considering the relationships between genetic variation and diseases. The database can also be economical for disease-association studies, as well as to facilitate an understanding of the processes which cause disease. Currently, the database contains 14,674 SNP records and 109,715 gene records associated with human diseases and it is updated at regular intervals.</p

EFFECTS OF PROBODY MASSAGE ON PHYSICAL CHARACTERISTICS, BODY ALIGNMENT IN THE MIDDLE-AGED WOMEN WITH MUSCULOSKELETAL DISEASES

The purpose of this study was to investigate the degree of improvement of physical characteristics, body alignment of the exercise group after Probody Massage Program of 8 weeks with 30 musculoskeletal diseases in middle-aged Women in B Metropolitan city. The subjects of this study were 30 musculoskeletal diseases in middle-aged in B Metropolitan city for 8 weeks twice a week, was carried out the Probody Massage Program of 60 minutes. Physiological characteristics are height, weight, BMI, an index of inflammation, body alignment was measured pretest, after 8 weeks. As the Probody Massage Program was showed a positive change in physical characteristics, body alignment with musculoskeletal diseases in middle-aged Women. Consequently it was suggested that Probody Massage with improvement and prevention for posture's unbalance of musculoskeletal diseases in middle-aged Women. This program could be utilized for improvement of youth postures and physical characteristics, body alignment of musculoskeletal diseases in middle-aged Women

GS2PATH: A web-based integrated analysis tool for finding functional relationships using gene ontology and biochemical pathway data

GS2PATH is a Web-based pipeline tool to permit functional enrichment of a given gene set from prior knowledge databases, including gene ontology (GO) database and biological pathway databases. The tool also provides an estimation of gene set enrichment, in GO terms, from the databases of the KEGG and BioCarta pathways, which may allow users to compute and compare functional over-representations. This is especially useful in the perspective of biological pathways such as metabolic, signal transduction, genetic information processing, environmental information processing, cellular process, disease, and drug development. It provides relevant images of biochemical pathways with highlighting of the gene set by customized colors, which can directly assist in the visualization of functional alteration

Effective Dispersion of MgO Nanostructure on Biochar Support as a Basic Catalyst for Glucose Isomerization

Glucose isomerization to fructose is one of the most important reactions in the field of biomass valorization. We demonstrate wood waste valorization with MgCl2 salt to synthesize an environment-friendly catalyst (i.e., MgO-biochar), which exhibits effective glucose-to-fructose isomerization with over 30% fructose yield and 80% selectivity at only 100 °C for 30 min in water as a green medium. This study highlights that one-step synthesis can effectively disperse and tether MgO nanostructures to the biochar matrix, which displays a significant reduction of Mg leaching compared to MgO-biochars produced by two-step synthesis and pure MgO. The MgCl2 acts as a porogen that facilitates the formation of a porous biochar structure and dispersion of nanostructured MgO. We identify key parameters of impregnation media (ethylene glycol, ethanol, and water) and pyrolysis conditions (600/750 °C in N2/CO2 atmosphere) that are responsible for adjusting the reactivity and stability of MgO, which enable the design of more effective and recyclable biochar catalysts. Weak interactions between MgCl2 and biomass in the presence of aqueous miscible organic solvents as shape-directing agents are accountable for fast leaching of Mg from the MgO-biochar surface. The FTIR spectra confirm the existence of various coordinations on the hydroxylated surfaces of MgO-biochar surfaces. The mesoporous structures of the biochar support enhance the stability of MgO moieties as revealed by BET, XRD, and Raman analyses. Given the benefits of effective MgO dispersion on the biochar support, we can reduce the amount of MgO active species involved in each reaction run, which mitigates over-reaction compared to pure MgO catalysts and achieves high fructose yield and selectivity for three consecutive cycles

Effects of a Postnatal Care Program on Self-efficacy, Self-management, and Glycemic Control in Women with Gestational Diabetes Mellitus

PURPOSE: To examine effects of a postnatal care program on self-efficacy, self-management, and glycemic control in women with gestational diabetes mellitus (GDM). METHODS: A non-equivalent control group non-synchronized quasi-experimental design was used. Sixty-two women with GDM were enrolled and assigned to either an experimental group (n=30) or a control group (n=32). The experimental group received an intervention which was postnatal care program for women with GDM. The postnatal care program for GDM included an individual education with leaflet and mobile web-based video with three times of telephone counseling. Effects of the intervention were measured with self-efficacy, self-management questionnaire, and a 75 g oral glucose tolerance test (75g OGTT). Statistical significance was examined using independent t-test and χ2-test. RESULTS: Although there was no significant difference in 75g OGTT (χ2=.11, p=.748) or self-management (t=−1.28, p=.206), there was a statistically significant increase in self-efficacy (t=−2.02, p=.048) in the experimental group compared to that in the control group. CONCLUSION: A postnatal care program is needed for women with GDM to improve their self-efficacy. Further studies are warranted to improve self-management and glycemic control through tailored education for GDM postpartum women

A giant retroperitoneal lymphangioma in a patient with neurofibromatosis type 1

Neurofibromatosis type 1 (NF-1) is a genetically inherited disorder that may cause skin abnormalities and tumors that form on nerve tissues. These tumors can be small or large and can occur anywhere in the body, including the brain, spinal cord, or other peripheral nerves. Retroperitoneal lymphangiomas are very rare benign malformations of the lymphatic system. About 95% lymphangiomas occur in the skin and the subcutaneous tissues of the head, neck and axillary region and the remaining 5% appear in other parts of the body such as lungs, pleura, pericardium, liver, gallbladder, kidney, and the mesentery. Herein, we report the case of a giant retroperitoneal lymphangioma in a patient with NF-1 with a review of the literature

The Evolutionarily Conserved LIM Homeodomain Protein LIM-4/LHX6 Specifies the Terminal Identity of a Cholinergic and Peptidergic C. elegans Sensory/Inter/Motor Neuron-Type

The expression of specific transcription factors determines the differentiated features of postmitotic neurons. However, the mechanism by which specific molecules determine neuronal cell fate and the extent to which the functions of transcription factors are conserved in evolution are not fully understood. In C. elegans, the cholinergic and peptidergic SMB sensory/inter/motor neurons innervate muscle quadrants in the head and control the amplitude of sinusoidal movement. Here we show that the LIM homeobox protein LIM-4 determines neuronal characteristics of the SMB neurons. In lim-4 mutant animals, expression of terminal differentiation genes, such as the cholinergic gene battery and the flp-12 neuropeptide gene, is completely abolished and thus the function of the SMB neurons is compromised. LIM-4 activity promotes SMB identity by directly regulating the expression of the SMB marker genes via a distinct cis-regulatory motif. Two human LIM-4 orthologs, LHX6 and LHX8, functionally substitute for LIM-4 in C. elegans. Furthermore, C. elegans LIM-4 or human LHX6 can induce cholinergic and peptidergic characteristics in the human neuronal cell lines. Our results indicate that the evolutionarily conserved LIM-4/LHX6 homeodomain proteins function in generation of precise neuronal subtypes

PDbase: a database of Parkinson's Disease-related genes and genetic variation using substantia nigra ESTs

Background: Parkinson's disease (PD) is one of the most common neurodegenerative disorders, clinically characterized by impaired motor function. Since the etiology of PD is diverse and complex, many researchers have created PD-related research resources. However, resources for brain and PD studies are still lacking. Therefore, we have constructed a database of PD-related gene and genetic variations using the substantia nigra (SN) in PD and normal tissues. In addition, we integrated PD-related information from several resources. Results: We collected the 6,130 SN expressed sequenced tags (ESTs) from brain SN normal tissues and PD patients SN tissues using full-cDNA library and normalized cDNA library construction methods from our previous study. The SN ESTs were clustered in 2,951 unigene clusters and assigned in 2,678 genes. We then found up-regulated 57 genes and down-regulated 48 genes by comparing normal and PD SN ESTs frequencies with over 0.9 cut-off probability of differential expression based on the Audic and Claverie method. In addition, we integrated disease-related information from public resources. To examine the characteristics of these PD-related genes, we analyzed alternative splicing events, single nucleotide polymorphism (SNP) markers located in the gene regions, repeat elements, gene regulation elements, and pathways and protein-protein interaction networks. Conclusion: We constructed the PDbase database to capture the PD-related gene, genetic variation, and functional elements. This database contains 2,698 PD-related genes through ESTs discovered from human normal and PD patients SN tissues, and through integrating several public resources. PDbase provides the mitochondrion proteins, microRNA gene regulation elements, single nucleotide polymorphisms (SNPs) markers within PD-related gene structures, repeat elements, and pathways and networks with protein-protein interaction information. The PDbase information can aid in understanding the causation of PD. It is available at http://bioportal.kobic.re.kr/PDbase/. Supplementary data is available at http://bioportal.kobic.re.kr/PDbase/suppl.jsp. &#169; 2009 Yang et al; licensee BioMed Central Ltdclose