An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

Background  

Tunicates have been recently revealed to be the closest living relatives of vertebrates. Yet, with more than 2500 described species, details of their evolutionary history are still obscure. From a molecular point of view, tunicate phylogenetic relationships have been mostly studied based on analyses of 18S rRNA sequences, which indicate several major clades at odds with the traditional class-level arrangements. Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups such as the Aplousobranchia, Appendicularia, and Thaliacea.     

GMDD: a database of GMO detection methods

Background  

Since more than one hundred events of genetically modified organisms (GMOs) have been developed and approved for commercialization in global area, the GMO analysis methods are essential for the enforcement of GMO labelling regulations. Protein and nucleic acid-based detection techniques have been developed and utilized for GMOs identification and quantification. However, the information for harmonization and standardization of GMO analysis methods at global level is needed.     

Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans

Background  

Comparative genomic data among organisms allow the reconstruction of their phylogenies and evolutionary time scales. Molecular timings have been recently used to suggest that environmental global change have shaped the evolutionary history of diverse terrestrial organisms. Living xenarthrans (armadillos, anteaters and sloths) constitute an ideal model for studying the influence of past environmental changes on species diversification. Indeed, extant xenarthran species are relicts from an evolutionary radiation enhanced by their isolation in South America during the Tertiary era, a period for which major climate variations and tectonic events are relatively well documented.     

Proliferative activity in the cerebellar external granular layer evaluated by bromodeoxyuridine labeling

We have optimised an indirect immunoperoxidase technique demonstrating bromodeoxyuridine (BrdU) incorporation into dividing cells for cerebellar tissue sections of four-day-old rats injected with this marker. This permits confident identification of granule-cell precursors engaged in DNA synthesis in the external granular layer of the developing cerebellum. Preservation of BrdU immunoreactivity is attained using methanol/acetic acid fixation and different pretreatments before immunostaining, while unlabeled nuclei can be recognized clearly after Feulgen or hematoxylin counterstaining. We established conditions to ensure satisfactory BrdU uptake without affecting cell-cycle progression during the postlabeling time period. The dose of BrdU employed provides saturation S-phase labeling from at least 1 h after BrdU delivery. Various kinetic parameters and phase durations have been determined in experiments involving a single injection or cumulative labeling sequences, and the cycle time was calculated based on two models of generative behavior: steady-state and exponential growth. The working hypothesis of steadystate kinetics can be adopted successfully if the existence of neuroblasts with different proliferation rates is taken into account.     

Convergence in Arthropod Assemblages with Various Restoration Approaches for Canadian Deciduous Forests

Silvicultural practices are traditionally aimed at increasing forest profits; however, recent approaches to forest conservation have broadened to include nature-based silviculture for regenerating forests. In southern Ontario (Canada), originally dominated by deciduous forests, conifer plantations were established on abandoned agricultural sites. Currently, there is an increasing interest to convert these conifer stands to a state that mimics the original deciduous forest. We investigated arthropod abundance, species richness of carabid beetles, and abundance of arthropod assemblages (trophic and prey groups) under five silvicultural treatments conducted to regenerate deciduous forests (the natural forest type) from the old conifer plantations. The treatments included: (1) uniform canopy removal; (2) uniform canopy removal and understory removal; (3) group canopy removal; (4) group canopy removal and understory removal; and (5) untreated control plots (relatively pure red pine). Insects were sampled annually using sweepnets and pitfall traps. Results revealed treatment effects on the abundance of Coleoptera, Heteroptera, herbivores, and small arthropods (<3 mm) caught in sweepnet samples, where plots subjected to group shelterwood removal and understory removal supported higher abundances than the control plots. There was no treatment effect on the abundance of other arthropod groups or on the species richness and abundance of carabid beetles. The silvicultural treatments used to encourage natural regeneration did not seem to affect arthropod food availability for insectivorous vertebrates. Thus, the type of silvicultural strategy used to convert pine plantations to a stage that mimics the natural deciduous forests had little overall impact on arthropods.     

A new AluI satellite DNA in the root-knot nematode Meloidogyne fallax: relationships with satellites from the sympatric species M. hapla and M. chitwoodi

A highly abundant satellite DNA comprising 20% of the Meloidogyne fallax (Nematoda, Tylenchida) genome was cloned and sequenced. The satellite monomer is 173 bp long and has a high A + T content of 72.3%, with frequent runs of A's and T's. The sequence variability of the monomers is 2.7%, mainly due to random distribution of single-point mutations. A search for evidence of internal repeated subunits in the monomer sequence revealed a 6-bp motif (AAATTT) for which five degenerated repeats, differing by just a single base pair, could be identified. Pairwise comparison of the M. fallax satellite with those from the sympatric species Meloidogyne chitwoodi and Meloidogyne hapla revealed a high sequence similarity (68.39%) with one satellite DNA subfamily in M. chitwoodi, which indicated an unexpected close relationship between them. Given the high copy number and the extreme sequence homogeneity among monomeric units, it may be assumed that the satellite DNA of M. fallax could have evolved through some recent and extensive amplification burst in the nematode genome. In this case, its relatively short life would not yet have allowed the accumulation of random mutations in independent amplified repeats. Considering the morphological resemblance between the two species and their ability to produce interspecific fertile hybrids under controlled conditions, these results indicate that M. fallax may share a common ancestor with M. chitwoodi, from which it could have diverged recently. All these data suggest that M. fallax could be the result of a recent speciation process and show that Meloidogyne satellite DNAs may be of interest to resolve phylogenetic relationships among closely related species from this genus.      

Can Zipf's law be adapted to normalize microarrays?

Background  

Normalization is the process of removing non-biological sources of variation between array experiments. Recent investigations of data in gene expression databases for varying organisms and tissues have shown that the majority of expressed genes exhibit a power-law distribution with an exponent close to -1 (i.e. obey Zipf's law). Based on the observation that our single channel and two channel microarray data sets also followed a power-law distribution, we were motivated to develop a normalization method based on this law, and examine how it compares with existing published techniques. A computationally simple and intuitively appealing technique based on this observation is presented.     

Matrix metalloproteinases as stromal effectors of human carcinoma progression: Therapeutic implications

The matrix metalloproteinases (MMPs) are extracellular zinc-enzymes implicated in a number of physiological and pathological tissue remodeling processes, including cancer progression. For a long time they have been thought to be produced by malignant cells and to specifically contribute to tumor invasion, through their ability to degrade extracellular matrix components. However, studies performed over the last few years have demonstrated that extracellular proteinases implicated in the progression of human carcinomas, including most MMPs, are in fact predominantly expressed by stromal and not by cancer cells. Furthermore, membrane receptors, activators and/or binding sites for some of these proteinases are also predominantly found to be associated with stromal cells. These findings, together with the observation that MMPs can cleave some molecules implicated in controlling growth factor activities, suggest that the role of MMPs during cancer progression is not limited to facilitating malignant cell invasion alone but is also likely to participate in other aspects of the malignant phenotype. MMPs should in fact be regarded as pan-regulators of tissue neoformation characteristic of malignant tumors, which includes both epithelial cell expansion and stroma formation. In this context, synthetic MMP inhibitors which are presently designed should lead to the development of a new generation of anticancer agents which additional beneficial properties compared to the existing cytotoxic agents used in the treatment of human malignancies.