Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs

Background  

The canonical core promoter elements consist of the TATA box, initiator (Inr), downstream core promoter element (DPE), TFIIB recognition element (BRE) and the newly-discovered motif 10 element (MTE). The motifs for these core promoter elements are highly degenerate, which tends to lead to a high false discovery rate when attempting to detect them in promoter sequences.     

Bipartite Tetracysteine Display Reveals Allosteric Control of Ligand-Specific EGFR Activation

Aberrant activation of the epidermal growth factor receptor (EGFR), a prototypic receptor tyrosine kinase, is critical to the biology of many common cancers. The molecular events that define how EGFR transmits an extracellular ligand binding event through the membrane are not understood. Here we use a chemical tool, bipartite tetracysteine display, to report on ligand-specific conformational changes that link ligand binding and kinase activation for full-length EGFR on the mammalian cell surface. We discover that EGF binding is communicated to the cytosol through formation of an antiparallel coiled coil within the intracellular juxtamembrane (JM) domain. This conformational transition is functionally coupled to receptor activation by EGF. In contrast, TGFα binding is communicated to the cytosol through formation of a discrete, alternative helical interface. These findings suggest that the JM region can differentially decode extracellular signals and transmit them to the cell interior. Our results provide new insight into how EGFR communicates ligand-specific information across the membrane.     

Toxic effects of copper sulfate on the brains of term Hubbard broiler chicks: a stereological and biochemical study

Copper sulfate can cause different pathologies in different organ systems during development. We determined the effects of toxic levels of copper sulfate on brain development in term Hubbard broiler chicks using stereological and biochemical analyses. Hubbard broiler chicken eggs were divided into three groups: controls with no treatment, sham-treated animals and an experimental group. On day 1, 0.1 ml saline was injected into the air chambers of the sham and experimental groups. The experimental group received also 50 μg copper sulfate. At term (day 21), all chick brains were removed and their volumes were determined using the Cavalieri volume estimation. Parallel biochemical analyses were carried out for glutathione and malondialdehyde levels in the brain tissues as indicators of oxidative damage. With copper treatment, the mean brain volume (8079 μm³) was significantly decreased compared to both the control (10075 μm³) and sham (9547 μm³) groups. Copper treatment (143.8 nmol/g tissue) showed significantly decreased malondialdehyde levels compared to the control (293.6 nmol/g tissue) and sham groups (268.8 nmol/g tissue). Copper treatment (404.5 nmol/g tissue) showed significantly increased malondialdehyde levels compared to the control (158.6 nmol/g tissue) and sham (142.8 nmol/g tissue) groups. The morphological and biochemical parameters we measured demonstrated that in term Hubbard broiler chicks, toxic levels of copper sulfate cause developmental and oxidative brain damage.     

Patterns of ribosomal RNA evolution in salamanders

Sequence comparisons are presented for four segments of the large subunit of ribosomal RNA, including divergent domains D7a and D7b, portions of the large divergent domains D2, D3, and D8, and evolutionarily conservative sequences flanking divergent domains. These results resolve phylogenetic relationships among exemplars of seven families of salamanders and the three amphibian orders. Phylogenetic analysis confirms the prediction that divergent domains feature the highest relative rates of base substitution and length variation within the ribosome, but the divergent domains evolve more slowly than nuclear noncoding DNA and the silent sites of structural genes. Base substitutions demonstrate approximately twice as many transitions as transversions and an uneven distribution among sites within the divergent domains but no apparent bias in base composition. Length mutations are primarily small insertions and deletions, with deletions predominating. The divergent domains appear to be a good source of phylogenetic information for evolutionary events occurring approximately 100-200 million years ago.      

Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring

Background  

The rapid and accurate identification of species is a critical component of large-scale biodiversity monitoring programs. DNA arrays (micro and macro) and DNA barcodes are two molecular approaches that have recently garnered much attention. Here, we compare these two platforms for identification of an important group, the mammals.     

The identification of informative genes from multiple datasets with increasing complexity

Background  

In microarray data analysis, factors such as data quality, biological variation, and the increasingly multi-layered nature of more complex biological systems complicates the modelling of regulatory networks that can represent and capture the interactions among genes. We believe that the use of multiple datasets derived from related biological systems leads to more robust models. Therefore, we developed a novel framework for modelling regulatory networks that involves training and evaluation on independent datasets. Our approach includes the following steps: (1) ordering the datasets based on their level of noise and informativeness; (2) selection of a Bayesian classifier with an appropriate level of complexity by evaluation of predictive performance on independent data sets; (3) comparing the different gene selections and the influence of increasing the model complexity; (4) functional analysis of the informative genes.