A comparative genomics study of genetic products potentially encoding ladderane lipid biosynthesis

Background  

The fatty acids of anaerobic ammonium oxidizing (anammox) bacteria contain linearly concatenated cyclobutane moieties, so far unique to biology. These moieties are under high ring strain and are synthesised by a presently unknown biosynthetic pathway.     

Analysis of cardiac signals using spatial filling index and time-frequency domain

Background  

Analysis of heart rate variation (HRV) has become a popular noninvasive tool for assessing the activities of the autonomic nervous system (ANS). HRV analysis is based on the concept that fast fluctuations may specifically reflect changes of sympathetic and vagal activity. It shows that the structure generating the signal is not simply linear, but also involves nonlinear contributions. These signals are essentially non-stationary; may contain indicators of current disease, or even warnings about impending diseases. The indicators may be present at all times or may occur at random in the time scale. However, to study and pinpoint abnormalities in voluminous data collected over several hours is strenuous and time consuming.     

Interactions between Mad1p and the nuclear transport machinery in the yeast Saccharomyces cerevisiae

In addition to its role in nucleocytoplasmic transport, the nuclear pore complex (NPC) acts as a docking site for proteins whose apparent primary cellular functions are unrelated to nuclear transport, including Mad1p and Mad2p, two proteins of the spindle assembly checkpoint (SAC) machinery. To understand this relationship, we have mapped domains of yeast Saccharomyces cerevisiae Mad1p that interact with the nuclear transport machinery, including further defining its interactions with the NPC. We showed that a Kap95p/Kap60p-dependent nuclear localization signal, positioned in the C-terminal third of Mad1p, is required for its efficient targeting to the NPC. At the NPC, Mad1p interacts with Nup53p and a presumed Nup60p/Mlp1p/Mlp2p complex through two coiled coil regions within its N terminus. When the SAC is activated, a portion of Mad1p is recruited to kinetochores through an interaction that is mediated by the C-terminal region of Mad1p and requires energy. We showed using photobleaching analysis that in nocodazole-arrested cells Mad1p rapidly cycles between the Mlp proteins and kinetochores. Our further analysis also showed that only the C terminus of Mad1p is required for SAC function and that the NPC, through Nup53p, may act to regulate the duration of the SAC response.     

Dephosphorylation of PKCdelta by protein phosphatase 2Ac and its inhibition by nucleotides

The protein phosphatases PP1(c), PP2A(c) and PP2Calpha are shown to dephosphorylate protein kinase Cdelta (PKCdelta) in vitro; of these PP2A(c) displayed the highest specific activity towards PKCdelta. The role of PP2A(c) in the dephosphorylation of PKCdelta in cells was supported by the demonstration that these proteins could be co-immunoprecipitated from NIH3T3 cells. However the observation that binding of Mg-ATP to PKCdelta could protect the enzyme from dephosphorylation by PP2A(c) in vitro indicates that an additional input/factor is required for dephosphorylation in vivo.     

Evolution of transposable elements: an IS10 insertion increases fitness in Escherichia coli

Strains of Escherichia coli carrying Tn10, a transposon consisting of two IS10 insertion sequences flanking a segment encoding for a tetracycline-resistance determinant, gain a competitive advantage in chemostat cultures. All Tn10-bearing strains that increase in frequency during competition have a new IS10 insertion that is found in the same location in the genome of those strains. We mapped, by a gradient of transmission, the position of the new IS10 insertion. We examined 11 isolates whose IS10 insertion was deleted by recombinational crossing- over, and in all cases the competitive fitness of the isolates was decreased. These results show that the IS10-generated insertion increases fitness in chemostat cultures. We named the insertion fit::IS10 and suggest that transposable elements may speed the rate of evolution by promoting nonhomologous recombination between preexisting variations within a genome and thereby generating adaptive variation.      

Subcellular localisation of the middle and large T-antigens of polyoma virus.

The distribution of two of the polyoma virus early proteins (the large and middle T-antigens) in lytically infected mouse cells and transformed rat cells has been investigated by indirect immunofluorescence and immuno-electron microscopy using well-characterised monoclonal antibodies. By these techniques, the viral large T-antigen was found almost exclusively in the nucleus, sometimes in association with nuclear pores, but never in the nucleolus. In lytically infected, but not transformed cells, fluorescence was detected in discrete areas ('hot spots') within the nucleus and, in a minor population of lytically infected cells, cytoplasmic immunoreactive material was observed. The viral middle T-antigen was found in association with most cytoplasmic membranes and in the majority of cells mainly in the endoplasmic reticulum. Only a fraction of the staining was observed in the plasma membrane and no staining in the nucleoplasm was observed. The data suggest that the site of action of the major transforming activity of polyoma virus need not be at the plasma membrane. Functions associated with the viral antigens are discussed in terms of their subcellular distributions within cells.     

Novel monoclonal antibodies that differentiate between the binding of pp60c-src or protein phosphatase 2A by polyomavirus middle T antigen.

Fourteen pGEX plasmids that express defined regions of polyomavirus middle T antigen in bacteria have been constructed. These polypeptides have been used to generate 18 new monoclonal antibodies directed against the unique portion of middle T and to map the approximate position of the antibody recognition sites onto the protein sequence. All of the antibodies effectively immunoprecipitate middle T and the associated 60- and 35-kDa components of protein phosphatase 2A. Four of the antibodies, however, do not react with middle T when it is bound to pp60c-src. These four probably bind to amino acids 203 to 218 of the middle T protein sequence, which are encoded by the mRNA immediately 3' to the splice junction that creates the C-terminal unique region. This suggests that additional middle T sequences are required for middle T's interaction with pp60c-src than are needed for its binding to protein phosphatase 2A. The antibodies localize this extra region and provide a means of distinguishing between these two associations.     

Specificity of siderophore-mediated transport of iron in rhizobia

The trihydroxamate siderophore, hydroxamate K, has been purified from culture filtrates of iron-deficient Rhizobium leguminosarum biovar viciae MNF710. The iron complex has a molecular weight of 828 and an absorption maximum at 443 nm (_M=1510). ⁵⁵Fe complexed to purified hydroxamate K was taken up by MNF710, its hydroxamate-negative mutant MNF7102 and Rhizobium leguminosarum biovar trifolii WU95 via an iron-regulated transport system, but Rhizobium meliloti U45 failed to take up the iron-siderophore complex under any conditions. A similar pattern of iron uptake was observed with ferrioxamine B. MNF710, MNF7102, U45 and WU95 all transported ⁵⁵Fe-ferrichrome but only the first three strains took up ⁵⁵Fe-ferrichrome A. All these ⁵⁵Fe-trihydroxamate uptake systems were ironregulated in MNF710, MNF7102 and WU95. In contrast, uptake of ⁵⁵Fe-rhodotorulate, a dihydroxamate, was essentially constitutive in all four organisms. Similarly, uptake of ⁵⁵Fe-citrate and ⁵⁵Fe-nitrilotriacetic acid was constitutive. None of the strains took up ⁵⁵Fe complexed with enterobactin or with pyoverdins from Pseudomonas aeruginosa ATCC15692 (PAO1) and Pseudomonas fluorescens ATCC17400.