SCOOP: a simple method for identification of novel protein superfamily relationships

MOTIVATION: Profile searches of sequence databases are a sensitive way to detect sequence relationships. Sophisticated profile-profile comparison algorithms that have been recently introduced increase search sensitivity even further. RESULTS: In this article, a simpler approach than profile-profile comparison is presented that has a comparable performance to state-of-the-art tools such as COMPASS, HHsearch and PRC. This approach is called SCOOP (Simple Comparison Of Outputs Program), and is shown to find known relationships between families in the Pfam database as well as detect novel distant relationships between families. Several novel discoveries are presented including the discovery that a domain of unknown function (DUF283) found in Dicer proteins is related to double-stranded RNA-binding domains. AVAILABILITY: SCOOP is freely available under a GNU GPL license from http://www.sanger.ac.uk/Users/agb/SCOOP/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

A simple probabilistic scoring method for protein domain identification

SUMMARY: A simple heuristic scoring method is described for assigning sequences to known domain types based on BLAST search outputs. The scoring is based on the score distribution of the known domain groups determined from a database versus database comparison and is directly applicable to BLAST output processing.     

Further considerations on the thermal stabilization of the nuclear matrix in mouse erythroleukemia cells.

The morphology and the polypeptide composition of the nuclear matrix obtained from 37 degrees C incubated nuclei has been studied in mouse erythroleukemia cells. From a structural point of view, in the absence of heat treatment, the matrix lacked identifiable nucleolar remnants and the internal fibrogranular meshwork whereas a peripheral lamina was seen. On the contrary, the matrix obtained from heat exposed nuclei displayed very electrondense nucleolar remnants and an abundant inner network. These results were obtained irrespective of the type of extracting agent (2M NaCl or 0.2 M (NH4)2SO4) used to remove histones and other soluble proteins. The heat stabilization of the matrix could not be prevented by sulfhydryl blocking chemicals such as iodoacetamide and n-ethylmaleimide, thus suggesting that heat does not stabilize the matrix by inducing the formation of disulfide bonds. Only limited differences in the polypeptide pattern of matrix isolated under different conditions were seen using one-dimensional pore gradient polyacrylamide gels stained with both Coomassie Brilliant Blue and silver despite the fact that the matrix fraction from heat treated nuclei retained about three fold more protein in comparison with controls. The same results were obtained also by means of two-dimensional non-equilibrium gel electrophoresis.     

A simple method for identification of gap-bridging subclones in DNA sequencing

A simple method for the identification of gap-bridging subclones in DNA sequencing is described.This work was carried out in the laboratory of Dr Johnston at the John Innes Institute, Norwich, NR4 7UH, UK.     

The identification of dimethylphenylarsine as a microbial metabolite using a simple method of chemofocusing

Candida humicola acts on benzenearsonic acid to produce dimethylphenylarsine, which was identified by mass spectroscopy following the chemofocusing of the volatile metabolite onto a mercuric chloride impregnated filter. The same technique established that trimethylarsine is the volatile metabolic product obtained from C. humicola treated with 4-NH₂-2-OHC₆H₃AsO(OH)₂ and (CH₃)₃AsO. Arsanilic acid, 4-NH₂C₆H₄AsO(OH)₂, is not metabolized to a volatile arsine.     

A simple PCR-RFLP method for identification and differentiation of 11 Malassezia species

A PCR-RFLP method targeted toward 26S rDNA and with 2 restriction enzymes, CfoI and BstF51, was developed to identify 11 Malassezia species. Not only type and standard strains but also 13 clinical isolates were identified successfully in this study. The results of identifications were confirmed by DNA sequencing.     

A simple matrix method for determining flux control coefficients in complex pathways

Flux control coefficients express in quantitative terms the extent to which the steady state flux through a metabolic pathway is controlled by a particular parameter. Enzyme flux control coefficients can be calculated using matrix algebra methods which express the control coefficients in terms of parameters which can be determined experimentally (enzyme elasticities, flux ratios, metabolite ratios). This paper describes an algorithm based on a 'constraint' matrix which enables expressions for enzyme control coefficients to be written for pathways of any complexity.     

Direct sectioning of unembedded cartilage: a simple method for microscopical and histochemical studies on chondrocytes and extracellular matrix

On account of the rigidity and compact structure of the hyaline cartilage, unfixed or formaldehyde fixed samples of this tissue can be directly sectioned by using a conventional ultramicrotome and a glass knife. This simple method allows to obtain microscopical sections from unembedded cartilage blocks, which show a well preserved histological structure and are very suitable to carry out morphological and histochemical studies on chondrocytes and cartilaginous matrix.     

A simple and rapid method for the differentiation and identification of thermophilic bacteria

In total, 170 strains of thermophilic bacteria were isolated from deep-sea hydrothermal fields in the Pacific Ocean and a hot spring in Xiamen of China. To facilitate the identification of thermophilic strains, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of whole-cell proteins of these strains was first performed. The results showed that there exist four different protein patterns, indicating that the 170 strains might belong to four species or genera. The RAPD (random amplified polymorphic DNA) profiles of nine representative strains were consistent with those of SDS-PAGE. To further identify the species of the nine strains, their 16S rDNA sequences were analyzed. The results showed that the nine strains fell into four species of three genera, which was the same as revealed by SDS-PAGE. Therefore, SDS-PAGE of whole-cell proteins could be used as a rapid and simple method for the discrimination of thermophilic bacteria as the first step of species identification.     

A simple method for the identification of higher taxa of picoplankton in water samples

A pigment analysis method using special divider mirrors andexcitation filters in conventional fluorescence microscopesis described. After fluorochromatization, this method can beused for reliably assigning microorganisms to different taxonomiclevels.     

Nanosized flower-like ZnO synthesized by a simple hydrothermal method and applied as matrix for horseradish peroxidase immobilization for electro-biosensing

Nanosized flower-like ZnO was synthesized by a simple hydrothermal method which is a convenient, environment friendly, inexpensive and efficient process. Raman spectroscopy, X-ray diffraction (XRD) and scanning electron microscope (SEM) were used to confirm the material structure and the crystallite microstructure. Then ZnO was dispersed in the chitosan solution to form a ZnO/chitosan composite matrix for the fabrication of H2O2 biosensor. This composite combined the advantages of inorganic species (ZnO) and organic polymer (chitosan). The parameters affecting the fabrication and experimental conditions of biosensors were optimized. Using hydroquinone as the mediator, the biosensor showed a fast response of less than 5s with the linear range of 1.0x10(-5) to 1.8x10(-3) M H2O2 with a correlation coefficient of 0.995 (n=20). The detection limit of the sensor was found to be 2.0 microM, based on a signal-to-noise ratio of 3. The biosensor exhibited satisfactory reproducibility and stability and retained about 78% of its original response after 40 days storage in a phosphate buffer at 4 degrees C.