SNP-RFLPing: restriction enzyme mining for SNPs in genomes

BACKGROUND: The restriction fragment length polymorphism (RFLP) is a common laboratory method for the genotyping of single nucleotide polymorphisms (SNPs). Here, we describe a web-based software, named SNP-RFLPing, which provides the restriction enzyme for RFLP assays on a batch of SNPs and genes from the human, rat, and mouse genomes. RESULTS: Three user-friendly inputs are included: 1) NCBI dbSNP "rs" or "ss" IDs; 2) NCBI Entrez gene ID and HUGO gene name; 3) any formats of SNP-in-sequence, are allowed to perform the SNP-RFLPing assay. These inputs are auto-programmed to SNP-containing sequences and their complementary sequences for the selection of restriction enzymes. All SNPs with available RFLP restriction enzymes of each input genes are provided even if many SNPs exist. The SNP-RFLPing analysis provides the SNP contig position, heterozygosity, function, protein residue, and amino acid position for cSNPs, as well as commercial and non-commercial restriction enzymes. CONCLUSION: This web-based software solves the input format problems in similar softwares and greatly simplifies the procedure for providing the RFLP enzyme. Mixed free forms of input data are friendly to users who perform the SNP-RFLPing assay. SNP-RFLPing offers a time-saving application for association studies in personalized medicine and is freely available at

V-MitoSNP: visualization of human mitochondrial SNPs

BACKGROUND: Mitochondrial single nucleotide polymorphisms (mtSNPs) constitute important data when trying to shed some light on human diseases and cancers. Unfortunately, providing relevant mtSNP genotyping information in mtDNA databases in a neatly organized and transparent visual manner still remains a challenge. Amongst the many methods reported for SNP genotyping, determining the restriction fragment length polymorphisms (RFLPs) is still one of the most convenient and cost-saving methods. In this study, we prepared the visualization of the mtDNA genome in a way, which integrates the RFLP genotyping information with mitochondria related cancers and diseases in a user-friendly, intuitive and interactive manner. The inherent problem associated with mtDNA sequences in BLAST of the NCBI database was also solved. DESCRIPTION: V-MitoSNP provides complete mtSNP information for four different kinds of inputs: (1) color-coded visual input by selecting genes of interest on the genome graph, (2) keyword search by locus, disease and mtSNP rs# ID, (3) visualized input of nucleotide range by clicking the selected region of the mtDNA sequence, and (4) sequences mtBLAST. The V-MitoSNP output provides 500 bp (base pairs) flanking sequences for each SNP coupled with the RFLP enzyme and the corresponding natural or mismatched primer sets. The output format enables users to see the SNP genotype pattern of the RFLP by virtual electrophoresis of each mtSNP. The rate of successful design of enzymes and primers for RFLPs in all mtSNPs was 99.1%. The RFLP information was validated by actual agarose electrophoresis and showed successful results for all mtSNPs tested. The mtBLAST function in V-MitoSNP provides the gene information within the input sequence rather than providing the complete mitochondrial chromosome as in the NCBI BLAST database. All mtSNPs with rs number entries in NCBI are integrated in the corresponding SNP in V-MitoSNP. CONCLUSION: V-MitoSNP is a web-based software platform that provides a user-friendly and interactive interface for mtSNP information, especially with regard to RFLP genotyping. Visual input and output coupled with integrated mtSNP information from MITOMAP and NCBI make V-MitoSNP an ideal and complete visualization interface for human mtSNPs association studies

Intermediate-mass black holes: finding of episodic, large-scale, and powerful jet activity in a dwarf galaxy

Dwarf galaxies are characterized by a very low luminosity and low mass. Because of significant accretion and ejection activity of massive black holes, some dwarf galaxies also host lo w-luminosity acti ve galactic nuclei (AGNs). In a few dwarf AGNs, very long baseline interferometry (VLBI) observations have found faint non-thermal radio emission. SDSS J090613.77 + 561015.2 is a dwarf AGN owning an intermediate-mass black hole (IMBH) with a mass of M-BH = 3 . 6 (+5.9) (-2.3 )x 10 (5) M(? )and showing a rarely seen two-component radio structure in its radio nucleus. To further probe their nature, i.e. the IMBH jet activity, we performed additional deep observations with the European VLBI Network (EVN) at 1.66 and 4.99 GHz. We find the more diffuse emission regions and structure details. These new EVN imaging results allow us to reveal a two-sided jet morphology with a size up to about 150 mas (projected length similar to 140 pc) and a radio luminosity of about 3 x 10( 38) erg s( -1). The peak feature has an optically thin radio spectrum and thus more likely represents a relatively young ejecta instead of a jet base. The EVN study on SDSS J090613.77 + 561015.2 demonstrates the existence of episodic, relatively large-scale, and powerful IMBH jet activity in dwarf AGNs. Moreo v er, we collected a small sample of VLBI-detected dwarf AGNs and investigated their connections with normal AGNs. We notice that these radio sources in the dwarf AGNs tend to have steep spectra and small linear sizes, and possibly represent ejecta from scaled-down episodic jet activity

Low-energy Spectra of the t-J-Type Models Studied by Variational Approach

We discuss recent progress of understanding the phenomena observed in high Tc cuprates by studying the d-wave resonating-valence-bond (d-RVB) based trial wave functions for the 2-dimensional t-J-type models. Treat exactly the strong correlation between electrons by numerical approach, we examine the evolution of ground states described by different variational wave functions and properties of the quasi-hole and -particle excitations of the d-RVB superconducting (SC) state. Properties related to the Fermi surface geometry deduced from quasi-hole energy dispersion of the SC state is shown to be consistent with the observation by photoemission spectroscopy. With the calculated spectral weights (SW's) for adding and removing an electron, we found not only the anti-correlation between conductance peak height and width between peaks seen in tunneling experiments, but also unique properties due to strong correlation which need to be verified by future experiments.Comment: 6 revtex pages with 5 (.eps) figures. To appear in a special volume of Journal of Magnetism and Magnetic Materials for the ICM 2006 proceeding

The Tevatron at the Frontier of Dark Matter Direct Detection

Direct detection of dark matter (DM) requires an interaction of dark matter particles with nucleons. The same interaction can lead to dark matter pair production at a hadron collider, and with the addition of initial state radiation this may lead to mono-jet signals. Mono-jet searches at the Tevatron can thus place limits on DM direct detection rates. We study these bounds both in the case where there is a contact interaction between DM and the standard model and where there is a mediator kinematically accessible at the Tevatron. We find that in many cases the Tevatron provides the current best limit, particularly for light dark matter, below 5 GeV, and for spin dependent interactions. Non-standard dark matter candidates are also constrained. The introduction of a light mediator significantly weakens the collider bound. A direct detection discovery that is in apparent conflict with mono-jet limits will thus point to a new light state coupling the standard model to the dark sector. Mono-jet searches with more luminosity and including the spectrum shape in the analysis can improve the constraints on DM-nucleon scattering cross section.Comment: 20 pages, 8 figures, final version in JHE

Bilateral Superficial Cervical Plexus Block Combined with General Anesthesia Administered in Thyroid Operations

We investigated the analgesic efficacy of bilateral superficial cervical plexus block in patients undergoing thyroidectomy and to determine whether it reduces the adverse effects of general anesthesia. We prospectively recruited 162 patients who underwent elective thyroid operations from March 2006 to October 2007. They were randomly assigned to receive a bilateral superficial cervical block (12 ml per side) with isotonic saline (group A; n = 56), bupivacaine 0.5% (group B; n = 52), or levobupivacaine 0.5% (group C; n = 54) after induction of general anesthesia. The analgesic efficacy of the block was assessed with: intraoperative anesthetics (desflurane), numbers of patients needing postoperative analgesics, the time to the first analgesics required, and pain intensity by visual analog scale (VAS). Postoperative nausea and vomiting (PONV) for 24 h were also assessed by the “PONV grade.” We also compared hospital stay, operative time, and discomfort in swallowing. There were no significant differences in patient characteristics. Each average end-tidal desflurane concentration was 5.8, 3.9, and 3.8% in groups A, B, and C, respectively (p < 0.001). Fewer patients in groups B and C required analgesics (A: B: C = 33:8:7; p < 0.001), and it took longer before the first analgesic dose was needed postoperatively (group A: B: C = 82.1:360.8:410.1 min; p < 0.001). Postoperative pain VAS were lower in groups B and C for the first 24 h postoperatively (p < 0.001). Incidences of overall and severe PONV were lower, however, there were not sufficient numbers of patients to detect differences in PONV among the three groups. Hospital stay was shorter in group B and group C (p = 0.011). There was no significant difference in operative time and postoperative swallowing pain among the three groups. Bilateral superficial cervical plexus block reduces general anesthetics required during thyroidectomy. It also significantly lowers the severity of postoperative pain during the first 24 h and shortens the hospital stay

Estimating Probable Maximum Precipitation and Probable Maximum Flood by Considering the Combined Effect of Typhoon and Monsoon Weather System under Climate Change

Source: ICHE Conference Archive - https://mdi-de.baw.de/icheArchive