The chloroplast generps 4 as a tool for the study ofPoaceae phylogeny

Phylogenetic analyses of 28Poaceae species based on the chloroplastrps 4 gene are presented using parsimony and distance methods. Two monocots from other families were used as outgroups. The chloroplast generps 4 was amplified, cloned, and sequenced for each species. The inferred phylogenetic trees were compared to recent classifications and are shown to fit their general features. There is a dichotomy in our tree between the pooid group and the other grasses. This is in contradiction with other molecular phylogenies, where the bamboos appear first within the family. This result led us to discuss some hypotheses about the relationships of the bambusoids with the other groups of grasses, and also about the relative position of rice and bamboo, which are found close to each other in our trees.     

The use of compensatory base change analysis of ITS2 as a tool in the phylogeny of Mucorales, illustrated by the Mucor circinelloides complex

Compensatory base changes (CBCs) in helix II of rDNA ITS2, suggested as a molecular classifier for fungi, were analyzed in Mucor circinelloides and its varieties. Only a few CBCs were found in the complex. Three out of the four accepted formae (f. circinelloides, f. lusitanicus, f. janssenii) did not exhibit CBCs. One CBC was found between strains that form zygospores; consequently, CBC is not always concordant with mating experiments. Strains with two CBC are unable to breed. It is suggested that some strains of the M. circinelloides complex are at the beginning of speciation.     

The use of neutron scattering to determine the functional structure of glycoside hydrolase

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The use of metabolomics as a tool to investigate hepatitis C

According to World Health Organization, an estimated 3 % of the global population is suffering from chronic hepatitis C. Furthermore, 60–70 % of chronically-infected patients develop liver diseases, of which 5–20 % of all cases advance to cirrhosis, and 1–5 % die from hepatitis C related hepatocellular carcinoma. This high incidence might be ascribed to the poor performance of the currently available diagnostic, treatment, and vaccination protocols, together with the lack of knowledge of the underlying disease mechanisms. In this review, we discuss the role that the relatively new research field termed metabolomics, alone or as part of an integrated ‘omics’ approach, has played in the investigation of hepatitis C and associated clinical manifestations. We also consider future research possibilities in this field, and the impact that these results might have on the fight against this global health predicament.     

Activity-based probes as a tool for functional proteomic analysis of proteases

Traditional proteomics methodology allows global analysis of protein abundance but does not provide information on the regulation of protein activity. Proteases, in particular, are known for their multilayered post-translational activity regulation that can lead to a significant difference between protease abundance levels and their enzyme activity. To address these issues, the field of activity-based proteomics has been established in order to characterize protein activity and monitor the functional regulation of enzymes in complex proteomes. In this review, we present structural features of activity-based probes for proteases and discuss their applications in proteomic profiling of various catalytic classes of proteases.     

Activity-based probes as a tool for functional proteomic analysis of proteases

Traditional proteomics methodology allows global analysis of protein abundance but does not provide information on the regulation of protein activity. Proteases, in particular, are known for their multilayered post-translational activity regulation that can lead to a significant difference between protease abundance levels and their enzyme activity. To address these issues, the field of activity-based proteomics has been established in order to characterize protein activity and monitor the functional regulation of enzymes in complex proteomes. In this review, we present structural features of activity-based probes for proteases and discuss their applications in proteomic profiling of various catalytic classes of proteases.     

Testate amoebae community analysis as a tool to assess biological impacts of peatland use

As most ecosystems, peatlands have been heavily exploited for different human purposes. For example, in Finland the majority is under forestry, agriculture or peat mining use. Peatlands play an important role in carbon storage, water cycle, and are a unique habitat for rare organisms. Such properties highlight their environmental importance and the need for their restoration. To monitor the success of peatland restoration sensitive indicators are needed. Here we test whether testate amoebae can be used as a reliable bioindicator for assessing peatland condition. To qualify as reliable indicators, responses in testate amoebae community structure to ecological changes must be stronger than random spatial and temporal variation. In this study, we simultaneously assessed differences between the effects of seasonality, intermediate scale spatial variation and land uses on living testate amoebae assemblages in natural, forested and restored peatlands. We expected the effects of seasonality on testate amoebae communities to be less pronounced than those of land use and within site variation. On average, natural sites harboured the highest richness and density, while the lowest numbers were found at forestry sites. Despite small changes observed in taxa dominance and differences in TA community structure between seasons and years at some sites, spatial heterogeneity, temperature, pH, nor water table depth seemed to significantly affect testate amoebae communities. Instead, observed differences were related to type of land use, which explained 75% of the community variation. Our results showed that testate amoebae community monitoring is a useful tool to evaluate impacts of human land use on boreal peatlands.     

Cryo-electron microscopy as an investigative tool: the ribosome as an example

Cryo-electron microscopy allows the visualization of macromolecules in their native state. Combined with techniques of three-dimensional reconstruction, cryo-EM images of single molecules can be used to study macromolecular interactions. The ribosome, a large RNA-protein complex with multiple binding interactions, is an excellent test case illustrating the power of these new techniques. Conformational changes during the binding of tRNA and protein factors to the ribosome can now be studied without the interference of crystal packing. Now that the first X-ray structures of ribosomal subunits have become available, conformational changes observed by cryo-EM in different functional states can be traced back to internal rearrangements of the underlying structural framework. Electron microscopy, X-ray crystallography, and modeling should be used together in the endeavor to understand the functioning of the translational machinery.     

Embryo transfer in the rat as a tool to determine genetic components of the gestational environment

Embryo transfer, with the recipient dam nursing the transferred progeny, was used to study the impact of the gestational environment on adult blood pressure (BP) in three inbred rat strains, the hypertensive Dahl salt-sensitive SS/JrCtr, the normotensive Dahl salt-hypertension resistant SR/Jr, and the normotensive Dark Agouti rat. Rats that had been cross-fostered within 6 h of birth were included as a control for lactational and nurturing factors. Systolic BP was measured by tail-cuff plethysmography twice a week in rats after the age of 7 weeks. Embryo transfer success, measured as the percentage of embryos transferred resulting in pups weaned at 4 weeks, was 27% between the SS/JrCtr and SR/Jr and 53% for the SS/JrCtr and Dark Agouti. This assessment included all failures, some of which probably were not associated with the transfer. If only the number of embryos transferred to dams with successful pregnancies was included, the success rate was 48% between the SS/JrCtr and SR/Jr and 82% between the SS/JrCtr and Dark Agouti strains. Anomalies in pups were not evident. In contrast to the lactational environment, the gestational milieu had a profound effect on basal blood pressure of the hypertensive SS/JrCtr progeny, less of an effect on that of the Dark Agouti, and no effect on that of the SR/Jr. Although the SS/JrCtr strain is significantly larger than the SR/Jr and Dark Agouti strains, neither embryo transfer nor cross-fostering altered body weight of rats at the age of 6 weeks. These data indicate that embryo transfer can be an easy and efficient method of isolating genetically determined factors of the gestational environment.     

Barnase fusion as a tool to determine the crystal structure of the small disulfide-rich protein McoEeTI

We present a fusion system suited to determine the crystal structure of small disulfide-rich proteins. McoEeTI, a hybrid inhibitor cystine knot microprotein, was produced as a soluble fusion to a catalytically inactive variant of the RNAse barnase in Escherichia coli. Functioning as a versatile tag, barnase facilitated purification, crystallization and high-resolution structure determination. Flexibility of the linker region allows for different relative orientations of barnase and the fusion partner in two crystallographically independent molecules and may thereby facilitate crystal packing. Nevertheless, the linker region is well ordered in both molecules. This system may prove more generally useful to determine the crystal structure of peptides and small proteins.     

The ribosome as a drug target

The elucidation of the crystal structure of the ribosome and its subunits has dramatically increased our understanding of this organelle and the molecular interactions that determine its functional capabilities. Two recent publications, one on the structure of the bacterial ribosome at 3.5A resolution and one on the identification of functionally relevant sites within the small subunit rRNA, illustrate the importance of interdisciplinary approaches in exploiting the ribosome as a drug target.     

The use of hypnosis as a tool in plastic surgery

Clinical hypnosis can be valuable tool for the plastic surgeon. Techniques can be rapidly learned at workshops that are held frequently at convenient locations throughout the country. Once misconceptions are dispelled, use of hypnosis is appropriate, safe, and effective.     

In vitro reconstitution of the GTPase-associated centre of the archaebacterial ribosome: the functional features observed in a hybrid form with Escherichia coli 50S subunits

We cloned the genes encoding the ribosomal proteins Ph (Pyrococcus horikoshii)-P0, Ph-L12 and Ph-L11, which constitute the GTPase-associated centre of the archaebacterium Pyrococcus horikoshii. These proteins are homologues of the eukaryotic P0, P1/P2 and eL12 proteins, and correspond to Escherichia coli L10, L7/L12 and L11 proteins respectively. The proteins and the truncation mutants of Ph-P0 were overexpressed in E. coli cells and used for in vitro assembly on to the conserved domain around position 1070 of 23S rRNA (E. coli numbering). Ph-L12 tightly associated as a homodimer and bound to the C-terminal half of Ph-P0. The Ph-P0.Ph-L12 complex and Ph-L11 bound to the 1070 rRNA fragments from the three biological kingdoms in the same manner as the equivalent proteins of eukaryotic and eubacterial ribosomes. The Ph-P0.Ph-L12 complex and Ph-L11 could replace L10.L7/L12 and L11 respectively, on the E. coli 50S subunit in vitro. The resultant hybrid ribosome was accessible for eukaryotic, as well as archaebacterial elongation factors, but not for prokaryotic elongation factors. The GTPase and polyphenylalanine-synthetic activity that is dependent on eukaryotic elongation factors was comparable with that of the hybrid ribosomes carrying the eukaryotic ribosomal proteins. The results suggest that the archaebacterial proteins, including the Ph-L12 homodimer, are functionally accessible to eukaryotic translation factors.     

The earliest evidence for the use of human bone as a tool

We report on the analysis of three human cranial fragments from a Mousterian context at the site of La Quina (France), which show anthropogenic surface modifications. Macroscopic and microscopic analyses, including SEM observation, demonstrate that the modifications visible on one of these fragments are similar to those produced on bone fragments used experimentally to retouch flakes. The microscopic analysis also identified ancient scraping marks, possibly resulting from the cleaning of the skull prior to its breakage and utilisation of a resulting fragment as a tool. The traces of utilisation and the dimensions of this object are compared to those on a sample of 67 bone retouchers found in the same excavation area and layer. Results show that the tool size, as well as the dimensions and location of the utilised area, fall well within the range of variation observed on faunal shaft fragments from La Quina that were used as retouchers. This skull fragment represents the earliest known use of human bone as a raw material and the first reported use of human bone for this purpose by hominins other than modern humans. The two other skull fragments, which probably come from the same individual, also bear anthropogenic surface modifications in the form of percussion, cut, and scraping marks. The deliberate versus unintentional hypotheses for the unusual choice of the bone are presented in light of contextual information, modifications identified on the two skull fragments not used as tools, and data on bone retouchers from the same layer, the same site, and other Mousterian sites.     

Ac as a tool for the functional genomics of rice

To examine whether the maize autonomous transposable element Ac can be used for the functional analysis of the rice genome, we used Southern blot analysis to analyze the behaviour of Ac in 559 rice plants of four transgenic families through three successive generations. All families showed highly active transposition of Ac, and 103 plants (18.4%) contained newly transposed Ac insertions. In nine of the 12 independent transpositions analyzed, their germinal transmission was detected. Partial sequencing of 99 Ac-flanking sequences revealed that 21 clones exhibited significant similarities with protein-coding genes in databases and four of them matched rice cDNA sequences. These results indicate preferential Ac transposition into protein-coding rice genes. To examine the feasibility of PCR-based screening of gene knockouts in rice Ac plants, we prepared bulked genomic DNA from the leaves of approximately 6000 rice Ac plants and pooled the DNA according to a three-dimensional matrix. Of 14 randomly selected genes, two gene knockouts were identified, and one encoding a rice cytochrome P450 (CYP86) gene was shown to be stably inherited to the progeny. Together, these results suggest that Ac can be efficiently used for the functional analysis of the rice genome.     

Fourier transform infrared spectroscopy as a new tool to determine rosmarinic acid in situ

A new procedure has been developed for the in situ FT-IR determination of rosmarinic acid (RA) in suspension cultures of Lavandula officinalis. The method involves sample preparation on ZnSe crystals or microplates from silicon, and measuring absorbance spectra between 4000 and 700 cm(-1). First derivative spectra were analysed after normalisation using partial least square (PLS) algorithm. The correlation between spectral analysis and HPLC measurements of cell extracts shows that the FT-IR procedure is suitable for qualitative and quantitative analyses of RA in cell suspension cultures.     

KH domains with impaired nucleic acid binding as a tool for functional analysis

In eukaryotes, RNA-binding proteins that contain multiple K homology (KH) domains play a key role in coordinating the different steps of RNA synthesis, metabolism and localization. Understanding how the different KH modules participate in the recognition of the RNA targets is necessary to dissect the way these proteins operate. We have designed a KH mutant with impaired RNA-binding capability for general use in exploring the role of individual KH domains in the combinatorial functional recognition of RNA targets. A double mutation in the hallmark GxxG loop (GxxG-to-GDDG) impairs nucleic acid binding without compromising the stability of the domain. We analysed the impact of the GDDG mutations in individual KH domains on the functional properties of KSRP as a prototype of multiple KH domain-containing proteins. We show how the GDDG mutant can be used to directly link biophysical information on the sequence specificity of the different KH domains of KSRP and their role in mRNA recognition and decay. This work defines a general molecular biology tool for the investigation of the function of individual KH domains in nucleic acid binding proteins.