Endogenous short RNAs generated by Dicer 2 and RNA-dependent RNA polymerase 1 regulate mRNAs in the basal fungus Mucor circinelloides

Endogenous short RNAs (esRNAs) play diverse roles in eukaryotes and usually are produced from double-stranded RNA (dsRNA) by Dicer. esRNAs are grouped into different classes based on biogenesis and function but not all classes are present in all three eukaryotic kingdoms. The esRNA register of fungi is poorly described compared to other eukaryotes and it is not clear what esRNA classes are present in this kingdom and whether they regulate the expression of protein coding genes. However, evidence that some dicer mutant fungi display altered phenotypes suggests that esRNAs play an important role in fungi. Here, we show that the basal fungus Mucor circinelloides produces new classes of esRNAs that map to exons and regulate the expression of many protein coding genes. The largest class of these exonic-siRNAs (ex-siRNAs) are generated by RNA-dependent RNA Polymerase 1 (RdRP1) and dicer-like 2 (DCL2) and target the mRNAs of protein coding genes from which they were produced. Our results expand the range of esRNAs in eukaryotes and reveal a new role for esRNAs in fungi.     

Conformational isomerism and hydrogen-bonded motifs of anion assisted supramolecular self-assemblies using Cu/Co salts and pyridine-4-acetamide

Six novel metal-organic complex assemblies constructed from a conformation-flexible ligand - pyridine-4-acetamide (PAT) and inorganic Cu^II and Co^II salts have been synthesized and structurally characterized by single crystal X-ray diffraction analysis. Crystal structure analysis reveals five types of architectures by variation of metal salts. In {[Cu(PAT)₂Cl₂]}_n (1) and {[Co(PAT)₂Cl₂]}_n (3), PAT ligands bridge metal centers to form one-dimensional chains. The chains are extended to three dimensions with the aid of two types of hydrogen bonded motifs () and (12)). {[Cu(PAT)₂(NO₃)](NO₃)(THF)}_n (5) which exhibits two-dimensional coordinating layers forms open channels filled with solvent molecules. In [Cu(PAT)₂Cl₂] (2), [Co(PAT)₂Cl₂] (4) and [Co(PAT)₄(H₂O)₂](NO₃)₂(THF)₂ (6), PAT is observed as a monofunctional ligand. Complex 2 forms one-dimensional hydrogen bonded chains. Crystal structure of complex 4 has a two-dimensional infinite hydrogen-bonded network with and motifs formed by complementary amide-amide hydrogen bonds. [Co(PAT)₄(H₂O)₂](NO₃)₂(THF)₂ (6) crystallizes in centrosymmetric I4₁/a space group. Complex 6 forms chiral channels which are filled with twisted solvent helices and anion helices. Within each channel the solvent helix and the anion helix have the same handedness; and adjacent channels have opposite handedness. Complexes 1, 2 and complexes 3, 4 illustrate examples of conformational supramolecular isomerism in {[Cu(PAT)₂Cl₂]}_∞ and {[Co(PAT)₂Cl₂]}_∞, respectively. In these complexes, changes of PAT conformations and coordination geometry of metal center induced the structural versatility.     

Revealing biological information using data structuring and automated learning

The intermediary steps between a biological hypothesis, concretized in the input data, and meaningful results, validated using biological experiments, commonly employ bioinformatics tools. Starting with storage of the data and ending with a statistical analysis of the significance of the results, every step in a bioinformatics analysis has been intensively studied and the resulting methods and models patented. This review summarizes the bioinformatics patents that have been developed mainly for the study of genes, and points out the universal applicability of bioinformatics methods to other related studies such as RNA interference. More specifically, we overview the steps undertaken in the majority of bioinformatics analyses, highlighting, for each, various approaches that have been developed to reveal details from different perspectives. First we consider data warehousing, the first task that has to be performed efficiently, optimizing the structure of the database, in order to facilitate both the subsequent steps and the retrieval of information. Next, we review data mining, which occupies the central part of most bioinformatics analyses, presenting patents concerning differential expression, unsupervised and supervised learning. Last, we discuss how networks of interactions of genes or other players in the cell may be created, which help draw biological conclusions and have been described in several patents.     

Functional genomics of the yeast DNA-damage response

High-throughput approaches are beginning to have an impact on many areas of yeast biology. Two recent studies, using different experimental platforms, provide insight into new pathways involved in the response of yeast to DNA damage.     

Using consensus networks to visualize contradictory evidence for species phylogeny

Building species phylogenies from genome data requires the evaluation of phylogenetic evidence from independent gene loci. We propose an approach to do this using consensus networks. We compare gene trees for eight yeast genomes and show that consensus networks have potential for helping to visualize contradictory evidence for species phylogenies.     

The tomato Cf-9 disease resistance gene functions in tobacco and potato to confer responsiveness to the fungal avirulence gene product avr 9

The Cf-9 gene encodes an extracytoplasmic leucine-rich repeat protein that confers resistance in tomato to races of the fungus Cladosporium fulvum that express the corresponding avirulence gene Avr 9. We investigated whether the genomic Cf-9 gene functions in potato and tobacco. Transgenic tobacco and potato plants carrying Cf-9 exhibit a rapid hypersensitive cell death response (HR) to Avr 9 peptide injection. Cf 9 tobacco plants were reciprocally crossed to Avr 9-producing tobacco. A developmentally regulated seedling lethal phenotype occurred in F1 progeny when Cf9 was used as the male parent and Avr 9 as the female parent. However, when Cf9 was inherited in the maternal tissue and a heterozygous Avr 9 plant was used as the pollen donor, a much earlier reaction was caused, leading to no germination of any F1 seed. Detailed analysis of the Avr 9-induced responses in Cf 9 tobacco leaves revealed that (1) most mesophyll cells died within 3 hr (compared with 12 to 16 hr in tomato); (2) the macroscopic HR was visible at an Avr 9 titer five times lower than that which caused visible symptoms in tomato; (3) the HR invariably extended into noninjected panels of the tobacco leaf; (4) no HR occurred in leaves of young tobacco plants; (5) in older plants, the HR was dramatically enhanced by sequential Avr 9 challenges; and (6) coexpression of a salicylate hydroxylase transgene (nahG) from Pseudomonas putida reduced the severity of the macroscopic leaf HR and also restored germination to Cf 9 x 35S:Avr 9 F1 seedlings. Simultaneous introduction of Cf-9 homologs (Hcr 9-9 genes A and B or D) along with the native Cf-9 gene did not alter the responses that were specifically induced by Avr 9. Various ways to use the Cf-9-Avr 9 gene combination to engineer broad-spectrum disease resistance in several solanaceous species are discussed.     

Ecomorphological pattern in Bermuda birds: The influence of competition and implications for nature preserves

Summary Previous ecomorphological studies of introduced land birds on oceanic islands have revealed several patterns consistent with the hypothesis that interspecific competition influenced the assembly process of that community. We extend one of these analyses to Bermuda, which differs from the previous islands in its size, latitude and isolation from the mainland. We tested for the presence of morphological overdispersion in surviving introduced passeriforms. Despite a possible predominance of random events in the assembly process due to Bermuda's small size and the presence of migrant species, the surviving passeriforms were morphologically overdispersed. The presence of this pattern supports the hypothesis that the assembly of the Bermuda passeriform community has been influenced by interspecific competition. This marks the third distinct community of island land birds in which this competitive pattern has been identified. This is particularly interesting because certain attributes of Bermuda and its avifauna make it more equivalent to communities in mainland refuges than avian assemblages on islands studied previously. This suggests that interspecific competition may have important effects on the structure of refuge communities.     

Chemotaxis by Pseudomonas aeruginosa.

Chemotaxis by Pseudomonas aeruginosa RM46 has been studied, and conditions required for chemotaxis have been defined, by using the Adler capillary assay technique. Several amino acids, organic acids, and glucose were shown to be attractants of varying effectiveness for this organism. Ethylenediaminetetraacetic acid was absolutely required for chemotaxis, and magnesium was also necessary for a maximum response. Serine taxis was greatest when the chemotaxis medium contained 1.5 X 10(-5) M ethylenediaminetetraacetic acid and 0.005 M magnesium chloride. It was not necessary to include methionine in the chemotaxis medium. The strength of the chemotactic responses to glucose and to citrate was dependent on prior growth of the bacteria on glucose and citrate, respectively. Accumulation in response to serine was inhibited by the addition of succinate, citrate, malate, glucose, pyruvate, or methionine to the chemotaxis medium. Inhibition by succinate was not dependent on the concentration of attractant in the capillary. However, the degree to which glucose and citrate inhibited serine taxis was dependent on the carbon source utilized for growth. Further investigation of this inhibition may provide information about the mechanisms of chemotaxis in P. aeruginosa.