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

Overexpression of Arabidopsis thaliana brassinosteroid-related acyltransferase 1 gene induces brassinosteroid-deficient phenotypes in creeping bentgrass

Brassinosteroids (BRs) are naturally occurring steroidal hormones that play diverse roles in various processes during plant growth and development. Thus, genetic manipulation of endogenous BR levels might offer a way of improving the agronomic traits of crops, including plant architecture and stress tolerance. In this study, we produced transgenic creeping bentgrass (Agrostis stolonifera L.) overexpressing a BR-inactivating enzyme, Arabidopsis thaliana BR-related acyltransferase 1 (AtBAT1), which is known to catalyze the conversion of BR intermediates to inactive acylated conjugates. After putative transgenic plants were selected using herbicide resistance assay, genomic integration of the AtBAT1 gene was confirmed by genomic PCR and Southern blot analysis, and transgene expression was validated by northern blot analysis. The transgenic creeping bentgrass plants exhibited BR-deficient phenotypes, including reduced plant height with shortened internodes (i.e., semi-dwarf), reduced leaf growth rates with short, wide, and thick architecture, high chlorophyll contents, decreased numbers of vascular bundles, and large lamina joint bending angles (i.e., erect leaves). Subsequent analyses showed that the transgenic plants had significantly reduced amounts of endogenous BR intermediates, including typhasterol, 6-deoxocastasterone, and castasterone. Moreover, the AtBAT1 transgenic plants displayed drought tolerance as well as delayed senescence. Therefore, the results of the present study demonstrate that overexpression of an Arabidopsis BR-inactivating enzyme can reduce the endogenous levels of BRs in creeping bentgrass resulting in BR-deficient phenotypes, indicating that the AtBAT1 gene from a dicot plant is also functional in the monocot crop.111Ysciescopu

A Family Harboring CMT1A Duplication and HNPP Deletion

Charcot-Marie-Tooth disease type 1A (CMT1A) is associated with duplication of chromosome 17p11.2-p12, whereas hereditary neuropathy with liability to pressure palsies (HNPP), which is an autosomal dominant neuropathy showing characteristics of recurrent pressure palsies, is associated with 17p11.2-p12 deletion. An altered gene dosage of PMP22 is believed to the main cause underlying the CMT1A and HNPP phenotypes. Although CMT1A and HNPP are associated with the same locus, there has been no report of these two mutations within a single family. We report a rare family harboring CMT1A duplication and HNPP deletion

Phenotypic Characterization of Transgenic Miscanthus sinensis Plants Overexpressing Arabidopsis Phytochrome B

Phytochromes are dimeric pigment proteins with reversible photochromism between red and far-red light-absorbing forms. They are photoreceptors that regulate various aspects of plant growth and development and have been used for biotechnological applications to improve agricultural performance of crops. Miscanthus species have been suggested as one of the most promising energy crops. In this paper, Arabidopsis phytochrome B (PHYB) gene was introduced into Miscanthus sinensis using Agrobacteriummediated transformation method that we developed recently, with the herbicide resistance gene (BAR) as a selection marker. After putative transgenic plants were selected using the herbicide resistance assay, genomic integration of the transgene was confirmed by genomic PCR and Southern blot analysis, and transgene expression was validated by Northern blot analysis. Compared to nontransformed control plants, transgenic plants overexpressing PHYB showed phenotypes with increased phytochrome B function, which includes increased chlorophyll content, decreased plant height, and delayed flowering. Therefore, these results suggest that Arabidopsis phytochrome B is functional in M. sinensis and provide a method to develop Miscanthus varieties with enhanced agricultural performance using phytochromes

Neuropathological changes in dorsal root ganglia induced by pyridoxine in dogs

Pyridoxine (PDX; vitamin B6), is an essential vitamin. PDX deficiency induces various symptoms, and when PDX is misused it acts as a neurotoxicant, inducing severe sensory neuropathy. To assess the possibility of creating a reversible sensory neuropathy model using dogs, 150 mg/kg of PDX was injected subcutaneously into dogs for 7 days and body weight measurements, postural reaction assessments, and electrophysiological recordings were obtained. In addition, the morphology of dorsal root ganglia (DRG) and changes in glial fibrillary acidic protein (GFAP) immunoreactive satellite glial cells and ionized calcium-binding adapter molecule 1 (Iba-1) immunoreactive microglia/macrophages were assessed at 1 day, 1 week, and 4 weeks after the last PDX treatment. During the administration period, body weight and proprioceptive losses occurred. One day after the last PDX treatment, electrophysiological recordings showed the absence of the H-reflex in the treated dogs. These phenomena persisted over the four post-treatment weeks, with the exception of body weight which recovered to the pre-treatment level. Staining (CV and HE) results revealed significant losses of large-sized neurons in the DRG at 1 day and 1 week after PDX treatment cessation, but the losses were recovered at 4 weeks post-treatment. The Iba-1 and GFAP immunohistochemistry results showed pronounced increases in reactive microglia/macrophage and satellite glial cell at 1 day and 1 week, respectively, after the last PDX treatment, and thereafter, immunoreactivity decreased with increasing time after PDX treatment. The results suggest that PDX-induced neuropathy is reversible in dogs; thus, dogs can be considered a good experimental model for research on neuropathy.This work was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Sci‑ ence, ICT & Future Planning (NRF-2017R1A1A1A05000762). The funding body played no role in the design and interpretation of the experiments. The found‑ ing sponsors had no role in the study design, performance, data collection and analysis, decision to publish, or preparation/writing of the manuscript

Protective effects of Scutellaria baicalensis Georgi against hydrogen peroxide-induced DNA damage and apoptosis in HaCaT human skin keratinocytes

Oxidative stress due to excessive accumulation of reactive oxygen species (ROS) is one of the risk factors for the development of several chronic diseases. In this study, we investigated the protective effects of Scutellaria bai- calensis rhizome ethanol extract (SBRE) against oxidative stress-induced cellular damage and elucidated the un- derlying mechanisms in the HaCaT human skin keratinocyte cell line. Our results revealed that treatment with SBRE prior to hydrogen peroxide (H2O2) exposure significantly increased viability of aCaT cells. SBRE also effectively attenuated H2O2-induced comet tail formation and inhibited the H2O2-induced phosphorylation levels of the histone γH2AX, as well as the number of apoptotic bodies and Annexin V-positive cells. In addition, SBRE exhibited scavenging activity against intracellular ROS generation and restored the mitochondrial membrane po- tential loss by H2O2. Moreover, H2O2 enhanced the cleavage of caspase-3 and degradation of poly (ADP-ribose)- polymerase, a typical substrate protein of activated caspase-3, as well as DNA fragmentation; however, these events were almost totally reversed by pretreatment with SBRE. Furthermore, SBRE increased the levels of heme oxygenase-1 (HO-1), which is a potent antioxidant enzyme, associated with the induction of nuclear fac- tor-erythroid 2-related factor 2 (Nrf2). According to our data, SBRE is able to protect HaCaT cells from H2O2- induced DNA damage and apoptosis through blocking cellular damage related to oxidative stress through a mech-anism that would affect ROS elimination and activating the Nrf2/HO-1 signaling pathway

Clinical Progress of Epilepsy in Children with Tuberous Sclerosis: Prognostic Factors for Seizure Outcome

The incidence and outcome of epilepsy in tuberous sclerosis (TS) patients have not yet been thoroughly investigated. The aim of this study was to evaluate the clinical features and prognosis of epileptic seizures associated with TS. The medical records of 29 patients who satisfied the diagnostic criteria for TS and were followed up for at least 2 years at the Department of Pediatrics, Chonnam National University Hospital (CNUH), between January 2000 and December 2010 were reviewed. Onset age of seizure, initial electroencephalography (EEG) findings, and efficacy of treatment were evaluated. Brain imaging studies were reanalyzed to determine the number of cortical tubers and subependymal nodules present. A total of 26 (89.6%) cases presented with seizures. In the seizure-controlled group (n=9, 34.6%), the mean number of cortical tubers was 4.5 (range, 0-16) and the mean number of subependymal nodules was 6.2 (range, 0-14). Initial EEG identified epileptiform discharges in 4 (44.5%) of these cases. In the seizure-sustained group (n=17, 58.6%), 10 patients had initial seizures before 1 year of age. In this group, the mean number of cortical tubers was 6.0 (range, 0-20) and the mean number of subependymal nodules was 6.0 (range, 1-11). A total of 15 (88.2%) had epileptiform discharges on their initial EEGs. In three patients who did not show any seizures during the observation period, the mean number of cortical tubers was 1.3 (range, 0-2), and the mean number of subependymal nodules was 4.6 (range, 0-13). Medical intractability of epilepsy in conjunction with TS did not correlate with age at onset of seizure, the number of cortical tubers, or subependymal nodules, but was associated with initial EEG findings

N-doped graphitic self-encapsulation for high performance silicon anodes in lithium-ion batteries

N-doped sites at CNT and graphene trigger spontaneous encapsulation of Si particles by simple pH control at room temperature. Significantly, N-doped CNT encapsulated Si composite electrode materials show remarkable cycle life and rate performance in battery operations. Superior capacity retention of 79.4% is obtained after 200 cycles and excellent rate capability of 914 mA h g -1 is observed at a 10 C rate.close13