Effect of Periodic Oscillations of Artificial Light Emission on Photosynthetic Activity

The effects of periodic oscillation of artificial light and of the frequency of these oscillations on photosynthetic assimilation has been measured. When the frequency is sufficiently high, the gross CO₂ assimilation in fluctuating light is identical to the assimilation of the leaf under a continuous illumination equal to the efficient intensity of the intermittent light. It is necessary to consider the quality of the sensor used for measuring light intensity, particularly its response velocity.     

Effects of habitat fragmentation on the timing of Crested Tit Parus cristatus natal dispersal

Crested Tit Parus cristatus young from first broods dispersed 1 week later if they were born in small isolated pine plots ('habitat fragments') compared with individuals in a large pine forest ('continuous habitat'). This delay in dispersal was caused by an extended period between fledging and dispersal. In second broods, the delay was even longer due to the interbrood interval being 9 days longer in habitat fragments. As nestlings in habitat fragments had a lower body-mass, and age at dispersal was negatively correlated with nestling body-mass within each nest, the postponed dispersal from fragments might be explained partly by a lower body-mass. Alternatively, postponed dispersal from fragments could result from a barrier effect caused by reluctance to cross inhospitable habitat.
Immigration by young from first broods into habitat fragments was delayed by approximately 3 weeks, and proportionally more second brood emigrants were recovered in this type of habitat. These results are in agreement with the hypothesis that fragments are second-choice habitat. Early immigrants into continuous habitat had a higher probability of settlement in winter flocks compared with late ones, independent of condition or age. Therefore, Crested Tits born in habitat fragments probably have a lower chance of settling in first-choice habitat.     

Sequence and functional analyses of Haemophilus spp. genomic islands

Background

A major part of horizontal gene transfer that contributes to the diversification and adaptation of bacteria is facilitated by genomic islands. The evolution of these islands is poorly understood. Some progress was made with the identification of a set of phylogenetically related genomic islands among the Proteobacteria, recognized from the investigation of the evolutionary origins of a Haemophilus influenzae antibiotic resistance island, namely ICEHin1056. More clarity comes from this comparative analysis of seven complete sequences of the ICEHin1056 genomic island subfamily.

Results

These genomic islands have core and accessory genes in approximately equal proportion, with none demonstrating recent acquisition from other islands. The number of variable sites within core genes is similar to that found in the host bacteria. Furthermore, the GC content of the core genes is similar to that of the host bacteria (38% to 40%). Most of the core gene content is formed by the syntenic type IV secretion system dependent conjugative module and replicative module. GC content and lack of variable sites indicate that the antibiotic resistance genes were acquired relatively recently. An analysis of conjugation efficiency and antibiotic susceptibility demonstrates that phenotypic expression of genomic island-borne genes differs between different hosts.

Conclusion

Genomic islands of the ICEHin1056 subfamily have a longstanding relationship with H. influenzae and H. parainfluenzae and are co-evolving as semi-autonomous genomes within the 'supragenomes' of their host species. They have promoted bacterial diversity and adaptation through becoming efficient vectors of antibiotic resistance by the recent acquisition of antibiotic resistance transposons.     

Evidence for a rapid rate of molecular evolution at the hypervariable and immunogenic Mycobacterium tuberculosis PPE38 gene region

Background  

PPE38 (Rv 2352c) is a member of the large PPE gene family of Mycobacterium tuberculosis and related mycobacteria. The function of PPE proteins is unknown but evidence suggests that many are cell-surface associated and recognised by the host immune system. Previous studies targeting other PPE gene members suggest that some display high levels of polymorphism and it is thought that this might represent a means of providing antigenic variation. We have analysed the genetic variability of the PPE38 genomic region on a cohort of M. tuberculosis clinical isolates representing all of the major phylogenetic lineages, along with the ancestral M. tuberculosis complex (MTBC) member M. canettii, and supplemented this with analysis of publicly available whole genome sequences representing additional M. tuberculosis clinical isolates, other MTBC members and non tuberculous mycobacteria (NTM). Where possible we have extended this analysis to include the adjacent plcABC and PPE39/40 genomic regions.     

Mutations in vimentin disrupt the cytoskeleton in fibroblasts and delay execution of apoptosis

To get new insights into the function of the intermediate filament (IF) protein vimentin in cell physiology, we generated two mutant cDNAs, one with a point mutation in the consensus motif in coil1A (R113C) and one with the complete deletion of coil 2B of the rod domain. In keratins and glia filament protein (GFAP), analogous mutations cause keratinopathies and Alexander disease, respectively. Both mutants prevented filament assembly in vitro and inhibited assembly of wild-type vimentin when present in equal amounts. In stably transfected preadipocytes, these mutants caused the complete disruption of the endogenous vimentin network, demonstrating their dominant-negative behaviour. Cytoplasmic vimentin aggregates colocalised with the chaperones alphaB-crystallin and HSP40. Moreover, vimR113C mutant cells were more resistant against staurosporine-induced apoptosis compared to controls. We hypothesise that mutations in the vimentin gene, like in most classes of IF genes, may contribute to distinct human diseases.     

Airborne Pollen Grains of Bozuyuk （Bilecik, Turkey）

Airborne pollen grains in the atmosphere of Bozuyuk were investigated over a 2 yr period from 2000 to 2001 using a Durham sampler. A total number of pollen grains of 5 170 pollen grains belonging to 32 taxa were identified and recorded along with some unidentified pollen grains. Of all the pollen grains, 78.66% were arboreal, 19.20% were non-arboreal, and 2.12% were unidentified. The majority of pollen grains investigated were Pinus, Platanus, Quercus, Cupressaceae, Poaceae, Fagus, Salix, Rosaceae, Urticaceae, Asteraceae, and Chenopodiaceae. The maximum number of pollen grains was recorded in May.     

Polymorphic microsatellites for the study of Aconitum napellus L. (Ranunculaceae), a rare species in France

Aconitum napellus is a perennial European Ranunculaceae that is currently decreasing in France. Six polymorphic microsatellite markers were characterized to study the polymorphism among individuals sampled from six populations in France. The total number of alleles per locus varied from two to four. Mean observed heterozygosities at each microsatellite locus ranged from 0.05 to 0.19. This set of microsatellites offers an efficient tool for more detailed investigations on population genetic structure of a rare species that can reproduce both sexually and by vegetative spread.     

Evolutionary dynamics of tandem repeats in the mitochondrial DNA control region of the minnow Cyprinella spiloptera

Length variation due to tandem repeats is now recognized as a common feature of animal mitochondrial DNA; however, the evolutionary dynamics of repeated sequences are not well understood. Using phylogenetic analysis, predictions of three models of repeat evolution were tested for arrays of 260-bp repeats in the cyprinid fish Cyprinella spiloptera. Variation at different nucleotide positions in individual repeats supported different models of repeat evolution. One set of characters included several nucleotide variants found in all copies from a limited number of individuals, while the other set included an 8- bp deletion found in a limited number of copies in all individuals. The deletion and an associated nucleotide change appear to be the result of a deterministic, rather than stochastic, mutation process. Parallel origins of repeat arrays in different mitochondrial lineages, possibly coupled with a homogenization mechanism, best explain the distribution of nucleotide variation.      

Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA

Secondary structure models are an important step for aligning sequences, understanding probabilities of nucleotide substitutions, and evaluating the reliability of phylogenetic reconstructions. A set of conserved sequence motifs is derived from comparative sequence analysis of 184 invertebrate and vertebrate taxa (including many taxa from the same genera, families, and orders) with reference to a secondary structure model for domain III of animal mitochondrial small subunit (12S) ribosomal RNA. A template is presented to assist with secondary structure drawing. Our model is similar to previous models but is more specific to mitochondrial DNA, fitting both invertebrate and vertebrate groups, including taxa with markedly different nucleotide compositions. The second half of the domain III sequence can be difficult to align precisely, even when secondary structure information is considered. This is especially true for comparisons of anciently diverged taxa, but well-conserved motifs assist in determining biologically meaningful alignments. Patterns of conservation and variability in both paired and unpaired regions make differential phylogenetic weighting in terms of "stems" and "loops" unsatisfactory. We emphasize looking carefully at the sequence data before and during analyses, and advocate the use of conserved motifs and other secondary structure information for assessing sequencing fidelity.