Size Does Matter: Cre-mediated Somatic Deletion Efficiency Depends on the Distance Between the Target <Emphasis Type="Italic">lox</Emphasis>-Sites

Cre/lox recombination in vivo has become an important tool to induce chromosomal rearrangements like deletions. Using a combination of Ds transposition and Cre/lox recombination in two independent experiments on chromosomes 6 and 7 of tomato, two sets of somatic deletions up to a size of 200 kb were obtained. The efficiency of somatic deletion decreased with increasing deletion size. The largest germinally transmitted deletion had a size of only 55 kb. The results show that Cre-mediated deletion in somatic cells is less efficient when the lox sites are separated over larger distances. A further drop of the deletion efficiency after germinal transmission of the larger deletions can be explained by the probable loss of genes that are of vital importance to gametophyte function. Plasmid rescue of an 8.4 kb circularised deleted DNA showed that the Cre-mediated deletion takes place in tomato as expected. Since the circular Cre-deleted DNA could only be PCR amplified in plant cells where the deletion was not complete, the double-stranded DNA circle is assumed to be instable.     

Characterization of the carboxysomal carbonic anhydrase CsoSCA from Halothiobacillus neapolitanus

In cyanobacteria and many chemolithotrophic bacteria, the CO(2)-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is sequestered into polyhedral protein bodies called carboxysomes. The carboxysome is believed to function as a microcompartment that enhances the catalytic efficacy of RubisCO by providing the enzyme with its substrate, CO(2), through the action of the shell protein CsoSCA, which is a novel carbonic anhydrase. In the work reported here, the biochemical properties of purified, recombinant CsoSCA were studied, and the catalytic characteristics of the carbonic anhydrase for the CO(2) hydration and bicarbonate dehydration reactions were compared with those of intact and ruptured carboxysomes. The low apparent catalytic rates measured for CsoSCA in intact carboxysomes suggest that the protein shell acts as a barrier for the CO(2) that has been produced by CsoSCA through directional dehydration of cytoplasmic bicarbonate. This CO(2) trap provides the sequestered RubisCO with ample substrate for efficient fixation and constitutes a means by which microcompartmentalization enhances the catalytic efficiency of this enzyme.     

Unconventional repertoire profile is imprinted during acute chikungunya infection for natural killer cells polarization toward cytotoxicity

Chikungunya virus (CHIKV) is a worldwide emerging pathogen. In humans it causes a syndrome characterized by high fever, polyarthritis, and in some cases lethal encephalitis. Growing evidence indicates that the innate immune response plays a role in controlling CHIKV infection. We show here that CHIKV induces major but transient modifications in NK-cell phenotype and function soon after the onset of acute infection. We report a transient clonal expansion of NK cells that coexpress CD94/NKG2C and inhibitory receptors for HLA-C1 alleles and are correlated with the viral load. Functional tests reveal cytolytic capacity driven by NK cells in the absence of exogenous signals and severely impaired IFN-γ production. Collectively these data provide insight into the role of this unique subset of NK cells in controlling CHIKV infection by subset-specific expansion in response to acute infection, followed by a contraction phase after viral clearance.     

Sequence context affects the rate of short insertions and deletions in flies and primates

Background  

Insertions and deletions (indels) are an important evolutionary force, making the evolutionary process more efficient and flexible by copying and removing genomic fragments of various lengths instead of rediscovering them by point mutations. As a mutational process, indels are known to be more active in specific sequences (like micro-satellites) but not much is known about the more general and mechanistic effect of sequence context on the insertion and deletion susceptibility of genomic loci.     

Rifampicin inactivation by Rhodococcus and Mycobacterium species

When prokaryotes are exposed to inhibitory concentrations of the antibiotic rifampicin, the only means hitherto identified by which cells overcome this inhibition is through mutational alteration in the target moiety, DNA-dependent RNA polymerase. In the nocardioform bacterium Rhodococcus erythropolis a novel mechanism has been identified, consisting of an inducible rifampicin-inactivating mechanism. Changes in the drug absorbance spectrum paralleled the decline in bacteriostatic activity of the antibiotic.     

Deoxyribonucleases of non-pathogenic corynebacteria

Fourteen species of non-pathogenic corynebacteria have been examined for the presence of DNases. Seven of the species were found to be DNase positive when assayed in Toluidine Blue-DNA-containing agar whereas only one, Corynebacterium callunae, could be detectable as DNase positive when the test was performed in DNA-methyl green-containing agar. Electrophoretic patterns obtained from sodium dodecyl sulfate-polyacrylamide gels containing DNA showed the presence of one or two bands of nucleolytic activity in two species of Brevibacterium and of several bands in C. callunae. Degradation of DNases by cellular proteases seem to occur in this species.     

Mitotic checkpoint gene expression is tuned by codon usage bias

The mitotic checkpoint (also called spindle assembly checkpoint, SAC) is a signaling pathway that safeguards proper chromosome segregation. Correct functioning of the SAC depends on adequate protein concentrations and appropriate stoichiometries between SAC proteins. Yet very little is known about the regulation of SAC gene expression. Here, we show in the fission yeast Schizosaccharomyces pombe that a combination of short mRNA half‐lives and long protein half‐lives supports stable SAC protein levels. For the SAC genes mad2 ⁺ and mad3 ⁺, their short mRNA half‐lives are caused, in part, by a high frequency of nonoptimal codons. In contrast, mad1 ⁺ mRNA has a short half‐life despite a higher frequency of optimal codons, and despite the lack of known RNA‐destabilizing motifs. Hence, different SAC genes employ different strategies of expression. We further show that Mad1 homodimers form co‐translationally, which may necessitate a certain codon usage pattern. Taken together, we propose that the codon usage of SAC genes is fine‐tuned to ensure proper SAC function. Our work shines light on gene expression features that promote spindle assembly checkpoint function and suggests that synonymous mutations may weaken the checkpoint.     

Spatial structure of a subtidal macrobenthic community in the Bay of Veys (western Bay of Seine, English Channel)

The spatial distribution of the muddy fine sand community from the Bay of Veys (western English Channel) were investigated during spring and autumn 1997. A grid of 55 and 54 sites was sampled in March and October, respectively, using two replicates per site of a Hamon grab (0.25 m²) for macrofauna collection and an additional one for sediment analysis. A total of 172 species were sampled with a dominance of polychaetes, followed by crustaceans and bivalves. The species richness and abundance show low temporal changes despite higher values in October than in March. In March, the mean abundance was 165 ind. 0.5 m⁻²; in October, the mean abundance was 212 ind. 0.5 m⁻². Four assemblages from the Abra alba-Pectinaria koreni community were identified corresponding to a bathymetric and sedimentary gradient from muddy fine sands with high levels of fine particles in shallow water to fine sands in deeper water. The discussion focuses on factors prevailing on the spatial structure of sandy communities in the English Channel.