PheMaDB: A solution for storage,retrieval, and analysis of high throughput phenotype data

Background  

OmniLog™ phenotype microarrays (PMs) have the capability to measure and compare the growth responses of biological samples upon exposure to hundreds of growth conditions such as different metabolites and antibiotics over a time course of hours to days. In order to manage the large amount of data produced from the OmniLog™ instrument, PheMaDB (Phenotype Microarray DataBase), a web-based relational database, was designed. PheMaDB enables efficient storage, retrieval and rapid analysis of the OmniLog™ PM data.     

Functional changes in human leukemic cell line HL-60. A model for myeloid differentiation

Polar solvents induce terminal differentiation in the human promyelocytic leukemia cell line HL-60. The present studies describe the functional changes that accompany the morphologic progression from promyelocytes to bands and poly-morphonuclear leukocytes (PMN) over 9 d of culture in 1.3 percent dimethylsulfoxide (DMSO). As the HL-60 cells mature, the rate of O(2-) production increase 18-fold, with a progressive shortening of the lag time required for activation. Hexosemonophosphate shunt activity rises concomitantly. Ingestin of paraffin oil droplets opsonized with complement or Ig increases 10-fold over 9 d in DMSO. Latex ingestion per cell by each morphologic type does not change significantly, but total latex ingestion by groups of cells increases with the rise in the proportion of mature cells with greater ingestion capacities. Degranulation, as measured by release of β-glucuronidase, lysozyme, and peroxidase, reaches maximum after 3-6 d in DMSO, then declines. HL-60 cells contain no detectable lactoferrin, suggesting that their secondary granules are absent or defective. However, they kill staphylococci by day 6 in DMSO. Morphologically immature cells (days 1-3 in DMSO) are capable of O(2-) generation, hexosemonophosphate shunt activity, ingestion, degranulation, and bacterial killing. Maximal performance of each function by cells incubated in DMSO for longer periods of time is 50-100 percent that of normal PMN. DMSO- induced differentiation of HL-60 cells is a promising model for myeloid development.     

Reproductive system,social organization,human disturbance and ecological dominance in native populations of the little fire ant,Wasmannia auropunctata

The invasive ant species Wasmannia auropunctata displays both ecologically dominant and non‐dominant populations within its native range. Three factors could theoretically explain the ecological dominance of some native populations of W. auropunctata: (i) its clonal reproductive system, through demographic and/or adaptive advantages; (ii) its unicolonial social organization, through lower intraspecific and efficient interspecific competition; (iii) the human disturbance of its native range, through the modification of biotic and abiotic environmental conditions. We used microsatellite markers and behavioural tests to uncover the reproductive modes and social organization of dominant and non‐dominant native populations in natural and human‐modified habitats. Microsatellite and mtDNA data indicated that dominant and non‐dominant native populations (supercolonies as determined by aggression tests) of W. auropunctata did not belong to different evolutionary units. We found that the reproductive system and the social organization are neither necessary nor sufficient to explain W. auropunctata ecological dominance. Dominance rather seems to be set off by unknown ecological factors altered by human activities, as all dominant populations were recorded in human‐modified habitats. The clonal reproductive system found in some populations of W. auropunctata may however indirectly contribute to its ecological dominance by allowing the species to expand its environmental niche, through the fixation over time of specific combinations of divergent male and female genotypes. Unicoloniality may rather promote the range expansion of already dominant populations than actually trigger ecological dominance. The W. auropunctata model illustrates the strong impact of human disturbance on species’ ecological features and the adaptive potential of clonal reproductive systems.     

A computational approach to characterization of bovine sperm chromatin alterations

We describe here a computational morphology-based approach to the investigation of possible causes of chromatin alterations in sperm. A comprehensive set of state-of-the-art and geometric measures are computationally extracted from toluidine blue stained images and analyzed to infer the possible processes leading to normal and abnormal chromatin formation while seeking a possible taxonomy of chromatin alterations and their influence on sperm head morphology. Using this methodology, we have identified higher chromatin fragility at some specific points of the sperm head. Despite the lack of correlation between morphologies of sperm head and chromatin structure, four main morphological types of chromatin alterations in bull spermatozoa have been identified and their possible causes discussed.     

Connectivity counts: disentangling effects of vegetation structure elements on the searching movement of a parasitoid

1. A heterogeneous habitat structure can have a profound impact on foraging carnivorous arthropods. In the present study, we examined which elements of complex vegetation structure influence the searching movement of a parasitoid model organism. 2. Previous field work showed that tall and dense vegetation reduces the parasitism success of the eulophid egg parasitoid Oomyzus galerucivorus while the probability of host egg deposition increased close to plant tips. 3. In laboratory bioassays, dried grass stems were arranged according to the natural situation in different setups. The wasps' walking time on stems increased with increasing stem height and density. High stem density decreased the walking time of the parasitoids on the ground and an increased stem height reduced the propensity to fly to the ground. Connectivity had a minor positive effect on the number of stem contacts, but considerably reduced the number of wasps reaching the upper part of grass stems by two‐thirds. 4. Thus, although enhanced vegetation complexity enhances walking activity of the parasitoids in the vegetation, laying eggs at the tip of long grass stems in dense vegetation can be an adaptive strategy for the host, as it maximises the number of connections between plant parts to cross by parasitoids before reaching the host. The connection points disorient the wasps, which lose time, reverse their direction or fly away.     

Attention and the detectability of weak taste stimuli

Subjects detected weak solutions of sucrose or citric acid under conditions in which attention was directed toward one of the tastants or the other. Detection thresholds were measured using an adaptive, forced-choice procedure, with a three-down one-up rule, which computer simulations suggest should be more reliable than the popular two-down one-up rule. The thresholds were modestly but systematically lower for attended tastants than for unattended ones. Similar results have been reported in other sense modalities, including vision (greater sensitivity to stimuli presented to attended versus unattended spatial locations) and hearing (greater sensitivity to stimuli presented at attended versus unattended sound frequencies). Taken together, the findings are consistent with a general hypothesis regarding attention in sensory systems: gains or losses in detectability occur when a central attentional mechanism (or, conceivably, a preattentive mechanism) selectively and preferentially monitors signals arising from particular subsets of peripheral neural inputs.      

Assessing the reliability of eBURST using simulated populations with known ancestry

Background  

The program eBURST uses multilocus sequence typing data to divide bacterial populations into groups of closely related strains (clonal complexes), predicts the founding genotype of each group, and displays the patterns of recent evolutionary descent of all other strains in the group from the founder. The reliability of eBURST was evaluated using populations simulated with different levels of recombination in which the ancestry of all strains was known.     

Two new species of Agatea (Violaceae) endemic to New Caledonia, with some taxonomic notes and a key to New Caledonian species

While working on a treatment of Violaceae for the Flore de Nouvelle-Caledonie et dependences , two new species were recognized, Agatea veillonii Munzinger and A. lecointei Munzinger. These species are here described and illustrated. Some taxonomic notes and a regional identification key are provided.