Automated screening and primer design of fish microsatellite DNA loci on pyrosequencing data

In recent years, massive sequencing approaches have allowed us to determine genomic structures of various organisms rapidly, raising novel applicability of the high-throughput sequence data obtained to various fields of biological studies. We present here a pipeline to search for microsatellite DNA and design PCR primers encompassing the microsatellites on genomic sequence data produced by 454 pyrosequencing. We tested this pipeline, called ‘Auto-primer’, on several fish genomic sequences and obtained many and various candidates for microsatellite DNA loci useful for detecting intraspecies genetic variability. This in silico search for microsatellite DNA is superior to conventional cloning methods, since any sequence patterns of repeat unit can be screened.     

Weather and the incidence of urinary stone colic in Tokyo

One hundred and thirty-four episodes of stone colic occurring in one center in 1984 were studied. Urinary stone formation was frequent in the hot season. Actual daily climatic factors which provoked the stone to cause colic were examined. Falling barometric pressure was followed by a high incidence of colic, and rising pressure was followed by a low incidence. Falling air temperature in the cold season and rising temperature in the hot season were associated with high incidence of colic.     

Group 12 metal complexes with inner-salt, bis(N,N-disubstituted amino)carbeniumdithiocarboxylate. Asymmetric stretching vibration of thiocarboxylate and reduction potential as probes for the coordination mode

A series of Group 12 metal complexes with bis(N,N-disubstituted amino)carbeniumdithiocarboxylates (RL) have prepared by the reaction of metal perchlorate with RL in EtOH or CH₂Cl_2, and characterized by the X-ray structural analysis, IR spectrum, and electrochemical measurements. The composition of metal and RL and the coordination mode, such as monodentate, chelate, and bridging or capping, depend on both the central metal ion and the substituent on the diaminocarbenium moiety. The useful criteria for the coordination mode are found to be the wavenumber of the -CS₂ asymmetric stretching vibration in the solid state, and the ligand-based reduction potential in solution.     

Alteration in density of eosinophils in the cerebrospinal fluid of mice infected with Angiostrongylus cantonensis

The density of eosinophils in the cerebrospinal fluid (CSF) and blood of male ddY mice infected with Angiostrongylus cantonensis was examined on days 14, 20 and 27 post-infection (p.i.) with discontinuous Percoll gradient centrifugation. Normal blood eosinophils had a density of between 1.070 and 1.080 g ml-1. No significant changes in density in blood eosinophils were noted during the course of the observations. CSF eosinophils began to become hypodense (defined as density less than 1.070 g ml-1) on day 20 p.i., and 88% of eosinophils were hypodense on day 27. Our results suggest therefore that eosinophils probably become hypodense in the CSF and brain tissues, but not in the blood.     

Reelin induces a radial glial phenotype in human neural progenitor cells by activation of Notch-1

Background  

Reelin and Notch-1 signaling pathways have been recently found to be necessary to induce the expression of brain lipid binding protein (BLBP) and to promote the process extension and the maturation of the neuronal progenitors, the radial glial cells. In this study, we report the cross talk between these two pathways.     

MLEP: an R package for exploring the maximum likelihood estimates of penetrance parameters

ABSTRACT: BACKGROUND: Linkage analysis is a useful tool for detecting genetic variants that regulate a trait of interest, especially genes associated with a given disease. Although penetrance parameters play an important role in determining gene location, they are assigned arbitrary values according to the researcher's intuition or as estimated by the maximum likelihood principle. Several methods exist by which to evaluate the maximum likelihood estimates of penetrance, although not all of these are supported by software packages and some are biased by marker genotype information, even when disease development is due solely to the genotype of a single allele. FINDINGS: Programs for exploring the maximum likelihood estimates of penetrance parameters were developed using the R statistical programming language supplemented by external C functions. The software returns a vector of polynomial coefficients of penetrance parameters, representing the likelihood of pedigree data. From the likelihood polynomial supplied by the proposed method, the likelihood value and its gradient can be precisely computed. To reduce the effect of the supplied dataset on the likelihood function, feasible parameter constraints can be introduced into maximum likelihood estimates, thus enabling flexible exploration of the penetrance estimates. An auxiliary program generates a perspective plot allowing visual validation of the model's convergence. The functions are collectively available as the MLEP R package. CONCLUSIONS: Linkage analysis using penetrance parameters estimated by the MLEP package enables feasible localization of a disease locus. This is shown through a simulation study and by demonstrating how the package is used to explore maximum likelihood estimates. Although the input dataset tends to bias the likelihood estimates, the method yields accurate results superior to the analysis using intuitive penetrance values for disease with low allele frequencies. MLEP is part of the Comprehensive R Archive Network and is freely available at http://cran.r-project.org/web/packages/MLEP/index.html.     

Isokuraramine and (−)-7,11-dehydromatrine,lupin alkaloids from flowers of Sophora flavescens

Two new lupin alkaloids, isokuraramine and (?)-7, 11-dihydromatrine, were isolated from the fresh flowers of Sophora flavescens along with 16 kno