An edit script for taxonomic classifications

Background  

The NCBI taxonomy provides one of the most powerful ways to navigate sequence data bases but currently users are forced to formulate queries according to a single taxonomic classification. Given that there is not universal agreement on the classification of organisms, providing a single classification places constraints on the questions biologists can ask. However, maintaining multiple classifications is burdensome in the face of a constantly growing NCBI classification.     

A taxonomic revision of Calotropis (Asclepiadaceae)

The genus Calotropis of the tribe Asclepiadeae of Asclepiadaceae subfamily Ascle-piadoideae is revised throughout its Tange in tropical and subtropical Africa and Asia. The three species recognized are keyed out, illustrated and described with appropriate bibliography, synonymy, notes on ecology, distribution and uses. Distribution maps for the species are provided. The taxonomic position of the genus is discussed and a historical review is provided.     

The effect of essential oils of basil on the growth of Aeromonas hydrophila and Pseudomonas fluorescens

Basil essential oils, including basil sweet linalool (BSL) and basil methyl chavicol (BMC), were screened for antimicrobial activity against a range of Gram-positive and Gram-negative bacteria, yeasts and moulds using an agar well diffusion method. Both essential oils showed antimicrobial activity against most of the micro-organisms examined except Clostridium sporogenes , Flavimonas oryzihabitans , and three species of Pseudomonas . The minimum inhibitory concentration (MIC) of BMC against Aeromonas hydrophila and Pseudomonas fluorescens in TSYE broth (as determined using an indirect impedance method) was 0·125 and 2% (v/v), respectively; the former was not greatly affected by the increase of challenge inoculum from 10³ to 10⁶ cfu ml⁻¹. Results with resting cells demonstrated that BMC was bactericidal to both Aer. hydrophila and Ps. fluorescens . The growth of Aer. hydrophila in filter-sterilized lettuce extract was completely inhibited by 0·1% (v/v) BMC whereas that of Ps. fluorescens was not significantly affected by 1% (v/v) BMC. In addition, the effectiveness of washing fresh lettuce with 0·1 or 1% (v/v) BMC on survival of natural microbial flora was comparable with that effected by 125 ppm chlorine.     

Biochemical Assessment of Serotonergic and Cholinergic Dysfunction and Cerebral Atrophy in Alzheimer's Disease

Abstract: Markers of serotonin synapses in entire temporal lobe and frontal and temporal neocortex were examined for changes in Alzheimer's disease by use of both neurosurgical and autopsy samples. Uptake of [³H]sero-tonin, binding of [³H]imipramine, and content of indola-mines were all significantly reduced, indicating that serotonin nerve terminals are affected. Binding of [³H]serotonin was also reduced, whereas that of [³H]qui-nuclidinyl benzilate, [³H]muscimol, and [³H]dihydroal-prenolol were unaltered. When the Alzheimer's samples were subdivided according to age, the reduction in [³H]serotonin binding was a feature of only autopsy samples from younger patients. In contrast, presynaptic cholinergic activity was reduced in all groups of Alzheimer's samples, including neurosurgical specimens. Five markers, thought to reflect cerebral atrophy, cytoplasm, nerve cell membrane, and neuronal perikarya were measured in the entire temporal lobe. In Alzheimer's disease the reductions (mean 25%, range 20–35%) were thought to be too large to be due only to loss of structures associated with the presumed cholinergic perikarya in the basal forebrain and monoamine neurones in the brain stem.     

TBMap: a taxonomic perspective on the phylogenetic database TreeBASE

Background  

TreeBASE is currently the only available large-scale database of published organismal phylogenies. Its utility is hampered by a lack of taxonomic consistency, both within the database, and with names of organisms in external genomic, specimen, and taxonomic databases. The extent to which the phylogenetic knowledge in TreeBASE becomes integrated with these other sources is limited by this lack of consistency.     

Cortical processing and perceived timing

As of yet, it is unclear how we determine relative perceived timing. One controversial suggestion is that timing perception might be related to when analyses are completed in the cortex of the brain. An alternate proposal suggests that perceived timing is instead related to the point in time at which cortical analyses commence. Accordingly, timing illusions should not occur owing to cortical analyses, but they could occur if there were differential delays between signals reaching cortex. Resolution of this controversy therefore requires that the contributions of cortical processing be isolated from the influence of subcortical activity. Here, we have done this by using binocular disparity changes, which are known to be detected via analyses that originate in cortex. We find that observers require longer stimulus exposures to detect small, relative to larger, disparity changes; observers are slower to react to smaller disparity changes and observers misperceive smaller disparity changes as being perceptually delayed. Interestingly, disparity magnitude influenced perceived timing more dramatically than it did stimulus change detection. Our data therefore suggest that perceived timing is both influenced by cortical processing and is shaped by sensory analyses subsequent to those that are minimally necessary for stimulus change perception.     

LSID Tester,a tool for testing Life Science Identifier resolution services

Background  

Life Science Identifiers (LSIDs) are persistent, globally unique identifiers for biological objects. The decentralised nature of LSIDs makes them attractive for identifying distributed resources. Data of interest to biodiversity researchers (including specimen records, images, taxonomic names, and DNA sequences) are distributed over many different providers, and this community has adopted LSIDs as the identifier of choice.     

Loss of meiosis in Aspergillus

If strictly mitotic asexual fungi lack recombination, the conventional view predicts that they are recent derivatives from older meiotic lineages. We tested this by inferring phylogenetic relationships among closely related meiotic and strictly mitotic taxa with Aspergillus conidial (mitotic) states. Phylogenies were constructed by using DNA sequences from the mitochondrial small ribosomal subunit, the nuclear ribosomal internal transcribed spacers, and the nuclear 5.8S ribosomal gene. Over 920 bp of sequence was analyzed for each taxon. Phylogenetic analysis of both the mitochondrial and nuclear data sets showed at least four clades that possess both meiotic and strictly mitotic taxa. These results support the hypothesis that strictly mitotic lineages arise frequently from more ancient meiotic lineages with Aspergillus conidial states. Many of the strictly mitotic species examined retained characters that may be vestiges of a meiotic state, including the production of sclerotia, sclerotium-like structures, and hulle cells.