Benzofuran based PDE4 inhibitors.

Replacement of the 3,4-dialkoxyphenyl substructure common to a number of PDE4 inhibitors with a 2-alkyl-7-methoxybenzofuran unit is described. This substitution can result in either enhancement or substantial reductions in PDE4 inhibitory activity depending on the system to which it is applied. An in vitro SAR study of a potent series of 4-(2-heteroaryl-ethyl)-benzoiurans 26 is also presented.     

Graphia: A platform for the graph-based visualisation and analysis of high dimensional data

Graphia is an open-source platform created for the graph-based analysis of the huge amounts of quantitative and qualitative data currently being generated from the study of genomes, genes, proteins metabolites and cells. Core to Graphia’s functionality is support for the calculation of correlation matrices from any tabular matrix of continuous or discrete values, whereupon the software is designed to rapidly visualise the often very large graphs that result in 2D or 3D space. Following graph construction, an extensive range of measurement algorithms, routines for graph transformation, and options for the visualisation of node and edge attributes are available, for graph exploration and analysis. Combined, these provide a powerful solution for the interpretation of high-dimensional data from many sources, or data already in the form of a network or equivalent adjacency matrix. Several use cases of Graphia are described, to showcase its wide range of applications in the analysis biological data. Graphia runs on all major desktop operating systems, is extensible through the deployment of plugins and is freely available to download from https://graphia.app/.     

Niche models tell half the story: spatial context and life‐history traits influence species responses to global change

Aim While niche models are typically used to assess the vulnerability of species to climate change, they have been criticized for their limited assessment of threats other than climate change. We attempt to evaluate this limitation by combining niche models with life‐history models to investigate the relative influence of climate change and a range of fire regimes on the viability of a long‐lived plant population. Specifically, we investigate whether range shift due to climate change is a greater threat to an obligate seeding fire‐prone shrub than altered fire frequency and how these two threatening processes might interact. Location Australian sclerophyll woodland and heathland. Methods The study species is Leucopogon setiger, an obligate seeding fire‐prone shrub. A spatially explicit stochastic matrix model was constructed for this species and linked with a dynamic niche model and fire risk functions representing a suite of average fire return intervals. We compared scenarios with a variety of hypothetical patches, a patch framework based upon current habitat suitability and one with dynamic habitat suitability based on climate change scenarios A1FI and A2. Results Leucopogon setiger was found to be sensitive to fire frequency, with shorter intervals reducing expected minimum abundances (EMAs). Spatial decoupling of fires across the landscape reduced the vulnerability of the species to shortened fire frequencies. Shifting habitat, while reducing EMAs, was less of a threat to the species than frequent fire. Main conclusions Altered fire regime, in particular more frequent fires relative to the historical regime, was predicted to be a strong threat to this species, which may reflect a vulnerability of obligate seeders in general. Range shifts induced by climate change were a secondary threat when habitat reductions were predicted. Incorporating life‐history traits into habitat suitability models by linking species distribution models with population models allowed for the population‐level evaluation of multiple stressors that affect population dynamics and habitat, ultimately providing a greater understanding of the impacts of global change than would be gained by niche models alone. Further investigations of this type could elucidate how particular bioecological factors can affect certain types of species under global change.     

Electroporation of cDNA/Morpholinos to targeted areas of embryonic CNS in <Emphasis Type="Italic">Xenopus</Emphasis>

Background  

Blastomere injection of mRNA or antisense oligonucleotides has proven effective in analyzing early gene function in Xenopus. However, functional analysis of genes involved in neuronal differentiation and axon pathfinding by this method is often hampered by earlier function of these genes during development. Therefore, fine spatio-temporal control of over-expression or knock-down approaches is required to specifically address the role of a given gene in these processes.     

Sequence, organization, and evolution of the A+T region of Drosophila melanogaster mitochondrial DNA

The long (4.6-kb) A+T region of Drosophila melanogaster mitochondrial DNA has been cloned and sequenced. The A+T region is organized in two large arrays of tandemly repeated DNA sequence elements, with nonrepetitive intervening and flanking sequences comprising only 22% of its length. The first repeat array consists of five repeats of 338-373 bp. The second consists of four intact 464-bp repeats and a fifth partial repeat of 137 bp. Three DNA sequence elements are found to be highly conserved in D. melanogaster and in several Drosophila species with short A+T regions. These include a 300-bp DNA sequence element that overlaps the DNA replication origin and two thymidylate stretches identified on opposite DNA strands. We conclude that the length heterogeneity observed in the A+T regulatory region in mitochondrial DNAs from the genus Drosophila results from the expansion (and contraction) of the number of repeated DNA sequence elements. We also propose that the 300-bp conserved DNA sequence element, in conjunction with another primary sequence determinant, perhaps the adjacent thymidylate stretch, functions in the regulation of mitochondrial DNA replication.      

Identification of Listeria monocytogenes Determinants Required for Biofilm Formation

Listeria monocytogenes is a Gram-positive, food-borne pathogen of humans and animals. L. monocytogenes is considered to be a potential public health risk by the U.S. Food and Drug Administration (FDA), as this bacterium can easily contaminate ready-to-eat (RTE) foods and cause an invasive, life-threatening disease (listeriosis). Bacteria can adhere and grow on multiple surfaces and persist within biofilms in food processing plants, providing resistance to sanitizers and other antimicrobial agents. While whole genome sequencing has led to the identification of biofilm synthesis gene clusters in many bacterial species, bioinformatics has not identified the biofilm synthesis genes within the L. monocytogenes genome. To identify genes necessary for L. monocytogenes biofilm formation, we performed a transposon mutagenesis library screen using a recently constructed Himar1 mariner transposon. Approximately 10,000 transposon mutants within L. monocytogenes strain 10403S were screened for biofilm formation in 96-well polyvinyl chloride (PVC) microtiter plates with 70 Himar1 insertion mutants identified that produced significantly less biofilms. DNA sequencing of the transposon insertion sites within the isolated mutants revealed transposon insertions within 38 distinct genetic loci. The identification of mutants bearing insertions within several flagellar motility genes previously known to be required for the initial stages of biofilm formation validated the ability of the mutagenesis screen to identify L. monocytogenes biofilm-defective mutants. Two newly identified genetic loci, dltABCD and phoPR, were selected for deletion analysis and both ΔdltABCD and ΔphoPR bacterial strains displayed biofilm formation defects in the PVC microtiter plate assay, confirming these loci contribute to biofilm formation by L. monocytogenes.     

Inhibition of DNA repair by trifluoperazine

We examined the possible role of calmodulin in the excision repair of ultraviolet light-induced pyrimidine dimers in damaged DNA by means of specialized assay systems. These assays included bromodeoxyuridine photolysis, dimer chromatography and cytosine arabinoside incorporation in conjunction with hydroxyurea. The calmodulin antagonist, trifluoperazine, and the calcium-chelating agent, EGTA, were employed to ascertain what affect calmodulin played in the repair process. Normal human fibroblast cells were used in all studies described in this report. After exposure to 10 J/m2 of 254 nm light, we observed a decrease of about 30% in the number of single-strand breaks produced in the presence of 25 microM trifluoperazine (1.9 vs. 3.3) in controls although the numbers of bases re-inserted in the repaired regions were similar (64 vs. 72). Measurement of thymine-containing dimers remaining throughout a 24 h time period indicated a 30% difference in the excision of dimers when tested with either EGTA or trifluoperazine. We also observed a significant decrease in the number of cytosine arabinoside arrested repair sites in the presence of either EGTA or trifluoperazine. The results are discussed with relation to the possibility of calmodulin altering the initial incision by repair endonuclease.