Populous: a tool for building OWL ontologies from templates

Background

Computing accurate nucleic acid melting temperatures has become a crucial step for the efficiency and the optimisation of numerous molecular biology techniques such as in situ hybridization, PCR, antigene targeting, and microarrays. MELTING is a free open source software which computes the enthalpy, entropy and melting temperature of nucleic acids. MELTING 4.2 was able to handle several types of hybridization such as DNA/DNA, RNA/RNA, DNA/RNA and provided corrections to melting temperatures due to the presence of sodium. The program can use either an approximative approach or a more accurate Nearest-Neighbor approach.

Results

Two new versions of the MELTING software have been released. MELTING 4.3 is a direct update of version 4.2, integrating newly available thermodynamic parameters for inosine, a modified adenine base with an universal base capacity, and incorporates a correction for magnesium. MELTING 5 is a complete reimplementation which allows much greater flexibility and extensibility. It incorporates all the thermodynamic parameters and corrections provided in MELTING 4.x and introduces a large set of thermodynamic formulae and parameters, to facilitate the calculation of melting temperatures for perfectly matching sequences, mismatches, bulge loops, CNG repeats, dangling ends, inosines, locked nucleic acids, 2-hydroxyadenines and azobenzenes. It also includes temperature corrections for monovalent ions (sodium, potassium, Tris), magnesium ions and commonly used denaturing agents such as formamide and DMSO.

Conclusions

MELTING is a useful and very flexible tool for predicting melting temperatures using approximative formulae or Nearest-Neighbor approaches, where one can select different sets of Nearest-Neighbor parameters, corrections and formulae. Both versions are freely available at http://sourceforge.net/projects/melting/and at http://www.ebi.ac.uk/compneur-srv/melting/under the terms of the GPL license.     

Changes to respiratory mechanisms during speech as a result of different cues to increase loudness.

The purpose of the present study was to determine whether different cues to increase loudness in speech result in different internal targets (or goals) for respiratory movement and whether the neural control of the respiratory system is sensitive to changes in the speaker's internal loudness target. This study examined respiratory mechanisms during speech in 30 young adults at comfortable level and increased loudness levels. Increased loudness was elicited using three methods: asking subjects to target a specific sound pressure level, asking subjects to speak twice as loud as comfortable, and asking subjects to speak in noise. All three loud conditions resulted in similar increases in sound pressure level . However, the respiratory mechanisms used to support the increase in loudness differed significantly depending on how the louder speech was elicited. When asked to target at a particular sound pressure level, subjects used a mechanism of increasing the lung volume at which speech was initiated to take advantage of higher recoil pressures. When asked to speak twice as loud as comfortable, subjects increased expiratory muscle tension, for the most part, to increase the pressure for speech. However, in the most natural of the elicitation methods, speaking in noise, the subjects used a combined respiratory approach, using both increased recoil pressures and increased expiratory muscle tension. In noise, an additional target, possibly improving intelligibility of speech, was reflected in the slowing of speech rate and in larger volume excursions even though the speakers were producing the same number of syllables.     

PhosphaBase: an ontology-driven database resource for protein phosphatases

PhosphaBase is an ontology-driven database resource containing information on the protein phosphatase family. It is the first public resource dedicated to protein phosphatases, which are enzymes that perform dephosphorylation reactions. In conjunction with the phosphorylation action of protein kinases, phosphatases are involved in important control and communication mechanisms in the cell. They have also been implicated in many human diseases, including diabetes and obesity, cancers, and neurodegenerative conditions. PhosphaBase aims to centralize the growing base of knowledge in the phosphatase research domain. The resource is built around a formal, domain-specific DAML+OIL ontology, and the data are collected from heterogeneous biological sources using Gene Ontology terms as a means of data extraction. The overall ontology-driven architecture provides a robust structure with distinct advantages for sustainability and provides the potential for the development of diagnostic tools, as well as a data repository.     

Pharmacological and electrophysiological characteristics of neurones in the paramedian reticular nucleus.

1. Neurones in the paramedian reticular nucleus of decerebrate, unanaesthetised cats have been identified by microelectrode recording combined with antidromic activation of their axons in the ipsilateral inferior cerebellar peduncle. Most paramedian reticular neurones were not influenced by somatic stimulation. 2. When applied by iontophoresis from multibarrelled micropipettes acetylcholine and 5-hydroxytryptamine excited all but a few paramedian reticular neurones while l-noradrenaline inhibited almost all the neurones investigated. The excitatory response to acetylcholine could be antagonised by gallamine. 3. The paramedian reticular nucleus appears to be a relatively homogeneous group of neurones, pharmacologically as well as anatomically.