Two natural cerato-ulmin (CU)-deficient mutants of Ophiostoma novo-ulmi: one has an introgressed O. ulmi cu gene, the other has an O. novo-ulmi cu gene with a mutation in an intron splice consensus sequence

The nucleotide sequences of the cerato-ulmin ( cu ) genes of two naturally occurring pathogenic CU-deficient mutants, PG470 and MAFf8, of the Dutch elm disease fungus, Ophiostoma novo-ulmi , were determined. The PG470  cu gene sequence was identical to that of CU-secreting isolates of O. novo-ulmi , except for a G to A mutation in the GT splice consensus sequence at the start of intron 1, suggesting that the CU deficiency was due to a splicing defect in the premRNA. In contrast, the MAFf8  cu gene showed a 99.1% sequence identity with cu genes of O. ulmi isolates, but only 92.8% sequence identity with cu genes of CU-secreting isolates of O. novo-ulmi , and in a dendrogram clustered with cu gene sequences of O. ulmi isolates with 100% bootstrap support. Restriction fragment length polymorphisms of the ribosomal RNA region, random amplified polymorphic DNA markers, and many biological properties of MAFf8, including pathogenicity, were typical of O. novo-ulmi . It is therefore likely that the cu gene of MAFf8 has been introgressed from O. ulmi , probably as a result of rare hybrid formation between O. ulmi and O. novo-ulmi , followed by backcrossing of the hybrid with O. novo-ulmi . The presence of an O. ulmi -like cu gene in MAFf8 is consistent with its CU deficiency, since the O. ulmi cu gene is known to be poorly expressed and O. ulmi isolates secrete little or no CU in culture.     

Sources of cell-to-cell variability in canonical nuclear factor-κB (NF-κB) signaling pathway inferred from single cell dynamic images

The canonical nuclear factor-κB (NF-κB) signaling pathway controls a gene network important in the cellular inflammatory response. Upon activation, NF-κB/RelA is released from cytoplasmic inhibitors, from where it translocates into the nucleus, subsequently activating negative feedback loops producing either monophasic or damped oscillatory nucleo-cytoplasmic dynamics. Although the population behavior of the NF-κB pathway has been extensively modeled, the sources of cell-to-cell variability are not well understood. We describe an integrated experimental-computational analysis of NF-κB/RelA translocation in a validated cell model exhibiting monophasic dynamics. Quantitative measures of cellular geometry and total cytoplasmic concentration and translocated RelA amounts were used as priors in Bayesian inference to estimate biophysically realistic parameter values based on dynamic live cell imaging studies of enhanced GFP-tagged RelA in stable transfectants. Bayesian inference was performed on multiple cells simultaneously, assuming identical reaction rate parameters, whereas cellular geometry and initial and total NF-κB concentration-related parameters were cell-specific. A subpopulation of cells exhibiting distinct kinetic profiles was identified that corresponded to differences in the IκBα translation rate. We conclude that cellular geometry, initial and total NF-κB concentration, IκBα translation, and IκBα degradation rates account for distinct cell-to-cell differences in canonical NF-κB translocation dynamics.     

Four phenotypically and phylogenetically distinct lineages in Phytophthora lateralis

Until recently Phytophthora lateralis was known only as the cause of dieback and mortality of Chamaecyparis lawsoniana in its native range in the Pacific Northwest (PNW). Since the 1990s however disease outbreaks have occurred increasingly on ornamental C. lawsoniana in Europe; and in 2007 the pathogen was discovered in soil around old growth Chamaecyparis obtusa in Taiwan, where it may be endemic. When the phenotypes of over 150 isolates of P. lateralis from Taiwan, across the PNW (British Columbia to California) and from France, the Netherlands and the UK were compared three growth rate groups were resolved: one slow growing from Taiwan, one fast growing from the PNW and Europe, and one of intermediate growth from a small area of the UK. Within these growth groups distinct subtypes were identified based on colony patterns and spore metrics and further discriminated in a multivariate analysis. The assumption that the three main growth groups represented phylogenetic units was tested by comparative sequencing of two mitochondrial and three nuclear genes. This assumption was confirmed. In addition two phenotype clusters within the Taiwan growth group were also shown to be phylogenetically distinct. These four phenotypically and genotypically unique populations are informally designated as the PNW lineage, the UK lineage, the Taiwan J lineage, and the Taiwan K lineage. Their characteristics and distribution are described and their evolution, taxonomic, and plant health significance is discussed.     

A possible billion-year-old holozoan with differentiated multicellularity

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Growth of synthetic stromatolites and wrinkle structures in the absence of microbes - implications for the early fossil record

Stromatolites and wrinkle structures are often taken to be an important indicator for early life. While both may be shaped by microbial mat growth, this can be open to doubt, so that the contribution of abiotic processes in their construction always needs to be established (Grotzinger & Knoll, 1999). We here report laboratory spray deposition experiments that can generate stromatolites and wrinkle structures in the absence of microbes. These minicolumnar and sometimes branched stromatolites are produced artificially by the aggregation of a synthetic colloid in a turbulent flow regime. They self-organize at the relatively low particle concentrations found in the outer parts of a spray beam. This contrasts with adjacent stratiform deposits that are produced by high rates of colloid deposition and relatively low sediment viscosities found in the centre of a spray beam. These stratiform laminae become subsequently wrinkled during hardening of the colloid. These results support numerical models that together suggest that physicochemical processes are capable of generating laminated sedimentary structures without the direct participation of biology. Geological environments where comparable abiogenic stromatolites and wrinkle structures may be found include: splash-zone silica sinters, desert varnish crusts and early Archean cherts formed from silica gel precursors.