Re‐forestation restores native dominance in an island beetle fauna

Native re‐forestation is a widely used restoration tool, typically undertaken with the expectation that planting native trees will initiate succession processes (including the re‐establishment of native fauna) that will eventually return the ecosystem to a native‐dominated state. Invertebrate groups can be used to assess restoration progress, as their life history traits enable them to respond more rapidly to environmental change than many other organisms. In this study, we assessed beetle responses to re‐forestation. Using two trapping methods (flight intercept traps and pitfall traps), we compared beetle assemblages in exotic pasture (pre‐restoration state), <10‐year‐old planted native forest (restoration intervention) and approximately 40‐year‐old unmanaged regenerating native forest (reference state). Analysis of the flight intercept‐trapped beetles suggests that re‐forestation has initiated a transition from an exotic‐dominated pasture fauna toward a native‐dominated fauna: in planted forests, 75% of all flight‐intercept‐trapped beetles were native (compared with 22% in pasture and 87% in unmanaged forest). Flight intercept‐trapped beetles also had higher native diversity and abundance in both forest types than in pasture. Pitfall‐trapped beetle species were predominantly native in both forest types, but there were few statistically significant differences between the forests and pasture in the pit‐fall trap data set. Both trapping methods detected significant compositional differences between the beetle assemblages in planted forest and unmanaged forest. Replanting native forest has increased native beetle diversity, abundance, and dominance (compared with the pre‐restoration state), but convergence with the unmanaged reference forest has not yet been achieved.     

160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)

Background  

To infer homology and subsequently gene function, the Smith-Waterman (SW) algorithm is used to find the optimal local alignment between two sequences. When searching sequence databases that may contain hundreds of millions of sequences, this algorithm becomes computationally expensive.     

Bactericidal action of positive and negative ions in air

Background  

In recent years there has been renewed interest in the use of air ionisers to control of the spread of airborne infection. One characteristic of air ions which has been widely reported is their apparent biocidal action. However, whilst the body of evidence suggests a biocidal effect in the presence of air ions the physical and biological mechanisms involved remain unclear. In particular, it is not clear which of several possible mechanisms of electrical origin (i.e. the action of the ions, the production of ozone, or the action of the electric field) are responsible for cell death. A study was therefore undertaken to clarify this issue and to determine the physical mechanisms associated with microbial cell death.     

The genetics of nuclear pre-mRNA splicing: a complex story

The occurrence of introns in nuclear precursor RNAs (pre-mRNAs) is widespread in eukaryotes, and the splicing process that removes them is basically the same in yeasts as it is in higher eukaryotes. Splicing takes place in a very large, multi-component complex, the spliceosome, and biochemical studies have been complicated by the large number of splicing factors involved. This review describes how genetic approaches used to study RNA splicing inSaccharomyces cerevisiae have complemented the biochemical studies and led to rapid advances in the field.     

The effect of biocides on proteins of Pseudomonas aeruginosa PAO bacteriophage F116

SDS-polyacrylamide gel electrophoresis (SDS-PAGE) was used to study the effect of several biocides on the protein content of Pseudomonas aeruginosa PAO phage F116. Eight major protein bands were identified and used as controls. The test biocides altered the control band pattern in different ways. Similarities were noticed between closely related biocides. Moreover, the alteration in the protein band pattern did not always correlate with phage inactivation.     

Down-regulation of serum/glucocorticoid regulated kinase 1 in colorectal tumours is largely independent of promoter hypermethylation

Background

We have previously shown that serum/glucocorticoid regulated kinase 1 (SGK1) is down-regulated in colorectal cancers (CRC) with respect to normal tissue. As hyper-methylation of promoter regions is a well-known mechanism of gene silencing in cancer, we tested whether the SGK1 promoter region was methylated in colonic tumour samples.

Methodology/Principal Findings

We investigated the methylation profile of the two CpG islands present in the promoter region of SGK1 in a panel of 5 colorectal cancer cell lines by sequencing clones of bisulphite-treated DNA samples. We further confirmed our findings in a panel of 10 normal and 10 tumour colonic tissue samples of human origin. We observed CpG methylation only in the smaller and more distal CpG island in the promoter region of SGK1 in both normal and tumour samples of colonic origin. We further identified a single nucleotide polymorphism (SNP, rs1743963) which affects methylation of the corresponding CpG.

Conclusions/Significance

Our results show that even though partial methylation of the promoter region of SGK1 is present, this does not account for the different expression levels seen between normal and tumour tissue.