Linear dichroism of single crystals of the reaction center from Rhodobacter sphaeroides wild type strain 2.4.1

The linear dichroism of single crystals of the photochemical reaction center from Rhodobacter sphaeroides 2.4.1, expressed as the anisotropy (or polarization) ratio, p = (A – A )/A + A , relative to the long morphological axis of the crystals, has been measured to be –0.12±0.03 for the primary donor Q _y and -0.15±0.8 for the carotenoid. These dichroic effects can be predicted using data obtained from magnetophotoselection (Frank et al. 1979, McGann and Frank 1985) and electron spin resonance (ESR)(Frank et al. 1988a, Budil et al. 1988) experiments. Magnetophotoselection data yield the projections of the transition moments onto the primary donor triplet state principal magnetic axis system. The single crystal triplet state ESR experiments provide the Euler matrix for the transformation from the principal magnetic axis system to the crystal unit cell axis system. Thus, the projections of the transition moments (site 1) onto the crystal units cell axes (a, b, c) are determined to be-0.39, 0.90 and 0.18, respectively. The projections of the carotenoid transition moment (site 1) onto the crystal unit cell axes (a, b, c) are determined to be -0.60, 0.02 and 0.80, respectively. This information used in conjunction with the crystalline space group symmetry (P₂₁2₁2₁) and the morphology of the crystals allows one to predict the observed anisotropy ratios.     

Profilin isoforms in Dictyostelium discoideum

Eukaryotic cells contain a large number of actin binding proteins of different functions, locations and concentrations. They bind either to monomeric actin (G-actin) or to actin filaments (F-actin) and thus regulate the dynamic rearrangement of the actin cytoskeleton. The Dictyostelium discoideum genome harbors representatives of all G-actin binding proteins including actobindin, twinfilin, and profilin. A phylogenetic analysis of all profilins suggests that two distinguishable groups emerged very early in evolution and comprise either vertebrate and viral profilins or profilins from all other organisms. The newly discovered profilin III isoform in D. discoideum shows all functions that are typical for a profilin. However, the concentration of the third isoform in wild type cells reaches only about 0.5% of total profilin. In a yeast-2-hybrid assay profilin III was found to bind specifically to the proline-rich region of the cytoskeleton-associated vasodilator-stimulated phosphoprotein (VASP). Immunolocalization studies showed similar to VASP the profilin III isoform in filopodia and an enrichment at their tips. Cells lacking the profilin III isoform show defects in cell motility during chemotaxis. The low abundance and the specific interaction with VASP argue against a significant actin sequestering function of the profilin III isoform.     

Robust consensus clustering for identification of expressed genes linked to malignancy of human colorectal carcinoma

Previous studies have been conducted in gene expression profiling to identify groups of genes that characterize the colorectal carcinoma disease. Despite the success of previous attempts to identify groups of genes in the progression of the colorectal carcinoma disease, their methods either require subjective interpretation of the number of clusters, or lack stability during different runs of the algorithms. All of which limits the usefulness of these methods. In this study, we propose an enhanced algorithm that provides stability and robustness in identifying differentially expressed genes in an expression profile analysis. Our proposed algorithm uses multiple clustering algorithms under the consensus clustering framework. The results of the experiment show that the robustness of our method provides a consistent structure of clusters, similar to the structure found in the previous study. Furthermore, our algorithm outperforms any single clustering algorithms in terms of the cluster quality score.     

Eco-floristic sectors and deforestation threats in Sumatra: identifying new conservation area network priorities for ecosystem-based land use planning

Biogeographical studies are a necessary step in establishing conservation area networks. Determining the ecological factors influencing vegetation is also a basic principle for hierarchical ecological classifications and a necessary prerequisite for ecosystem-based land use planning. Eco-floristic sectors (EFS) have already been identified for the Indonesian island of Sumatra, combining both approaches, dividing it into 38 EFSs representing unique ecosystems in terms of tree flora and environment (Laumonier 1997). The impact of deforestation on individual EFSs has been highly varied and in some cases extreme. We assigned one of five ‘extinction risk categories’ to each EFS based on the percentage of forest lost between 1985 and 2007. Eighty-five percent of all forest loss (10.2 million ha) occurred in the eastern peneplain, western lowland regions and swamps. In 2007, only 29% of forests were protected by conservation areas, only nine of the 38 EFS had more than 50% of their remaining forest cover protected. 38% of remaining forest was “critically endangered”, “endangered” or “vulnerable” EFSs (5 million ha) but only 1 million ha (20%) were protected. Sumatra’s existing network of conservation areas does not adequately represent the island’s ecosystems. Priorities for a new conservation area network can be formulated for integration into Sumatra’s new land use plans at provincial and district level. Decision makers can now use EFSs to locate new conservation areas so they represent and maintain the whole range of the island’s diversity.     

Enhanced Chlorella vulgaris Buitenzorg growth by photon flux density alteration in serial photobioreactors

Microalgae perform oxygenic photosynthesis and are capable of taking up a large amount of CO₂, using an inducible CO₂ concentrating mechanism (CCM), and fixing CO₂ into higher compounds. These characteristics make the microalgae potentially useful for removal and utilization of CO₂ emitted from industrial plants and, generally, the usage of photosynthetic microorganisms has increased and significantly improved as a solution for CO₂ emissions. In this light and based on previous research using Anabaena cylindrica IAM M1 and Spirulina platensis IAM M 135, enhancement was sought for CO₂ fixation and biomass production by Chlorella vulgaris Buitenzorg by increasing the photon flux density concurrent with increases in culture biomass during the cellular growth phase and was compared to cultures of Chlorella grown at optimal constant illumination, with all cultures grown using Bennick basal medium, 29°C, and a flow of 1.0 atm. 10% CO₂ enriched air delivered to three in serial photobioreactors of 0.200 dm³ capacity each. The results showed that increasing illumination during culture increased biomass production of Chlorella by ∼60% as well as increased CO₂ fixation ability by ∼7.0%. It was also demonstrated that the non-competitive inhibition of [HCO₃ ⁻] as a carbon source significantly affected the cultivation in both the increasing and constant photon flux density regimes.     

Defects in ErbB-Dependent Establishment of Adult Melanocyte Stem Cells Reveal Independent Origins for Embryonic and Regeneration Melanocytes

Adult stem cells are responsible for maintaining and repairing tissues during the life of an organism. Tissue repair in humans, however, is limited compared to the regenerative capabilities of other vertebrates, such as the zebrafish (Danio rerio). An understanding of stem cell mechanisms, such as how they are established, their self-renewal properties, and their recruitment to produce new cells is therefore important for the application of regenerative medicine. We use larval melanocyte regeneration following treatment with the melanocytotoxic drug MoTP to investigate these mechanisms in Melanocyte Stem Cell (MSC) regulation. In this paper, we show that the receptor tyrosine kinase, erbb3b, is required for establishing the adult MSC responsible for regenerating the larval melanocyte population. Both the erbb3b mutant and wild-type fish treated with the ErbB inhibitor, AG1478, develop normal embryonic melanocytes but fail to regenerate melanocytes after MoTP-induced melanocyte ablation. By administering AG1478 at different time points, we show that ErbB signaling is only required for regeneration prior to MoTP treatment and before 48 hours of development, consistent with a role in establishing MSCs. We then show that overexpression of kitla, the Kit ligand, in transgenic larvae leads to recruitment of MSCs, resulting in overproliferation of melanocytes. Furthermore, kitla overexpression can rescue AG1478-blocked regeneration, suggesting that ErbB signaling is required to promote the progression and specification of the MSC from a pre–MSC state. This study provides evidence that ErbB signaling is required for the establishment of adult MSCs during embryonic development. That this requirement is not shared with the embryonic melanocytes suggests that embryonic melanocytes develop directly, without proceeding through the ErbB-dependent MSC. Moreover, the shared requirement of larval melanocyte regeneration and metamorphic melanocytes that develops at the larval-to-adult transition suggests that these post-embryonic melanocytes develop from the same adult MSC population. Lastly, that kitla overexpression can recruit the MSC to develop excess melanocytes raises the possibility that Kit signaling may be involved in MSC recruitment during regeneration.     

The production of soluble pyrroloquinoline quinone glucose dehydrogenase by Klebsiella pneumoniae, the alternative host of PQQ enzymes

Klebsiella pneumoniae, which produces PQQ and is available for use with a conventional expression vector system, was selected as the host strain for soluble PQQ glucose dehydrogenase (PQQGDH-B) production. The recombinant K. pneumoniaeexpressed PQQGDH-B in its holo-form at about 18000 U l^–1, equal to that achieved in recombinant Escherichia coli. The signal sequence of recombinant PQQGDH-B produced by K. pneumoniaewas correctly processed. K. pneumoniaecan become an alternative host microorganism not only for PQQGDH-B production but also for recombinant PQQ enzymes production.     

Enolpyruvate transferase MurAAA149E,identified during adaptation of Enterococcus faecium to daptomycin,increases stability of MurAA–MurG interaction

Daptomycin (DAP) is an antibiotic frequently used as a drug of last resort against vancomycin-resistant enterococci. One of the major challenges when using DAP against vancomycin-resistant enterococci is the emergence of resistance, which is mediated by the cell-envelope stress system LiaFSR. Indeed, inhibition of LiaFSR signaling has been suggested as a strategy to “resensitize” enterococci to DAP. In the absence of LiaFSR, alternative pathways mediating DAP resistance have been identified, including adaptive mutations in the enolpyruvate transferase MurAA (MurAA^A149E), which catalyzes the first committed step in peptidoglycan biosynthesis; however, how these mutations confer resistance is unclear. Here, we investigated the biochemical basis for MurAA^A149E-mediated adaptation to DAP to determine whether such an alternative pathway would undermine the potential efficacy of therapies that target the LiaFSR pathway. We found cells expressing MurAA^A149E had increased susceptibility to glycoside hydrolases, consistent with decreased cell wall integrity. Furthermore, structure–function studies of MurAA and MurAA^A149E using X-ray crystallography and biochemical analyses indicated only a modest decrease in MurAA^A149E activity, but a 16-fold increase in affinity for MurG, which performs the last intracellular step of peptidoglycan synthesis. Exposure to DAP leads to mislocalization of cell division proteins including MurG. In Bacillus subtilis, MurAA and MurG colocalize at division septa and, thus, we propose MurAA^A149E may contribute to DAP nonsusceptibility by increasing the stability of MurAA–MurG interactions to reduce DAP-induced mislocalization of these essential protein complexes.     

Surface-sterilization of Glomus mosseae sporocarps for studying endomycorrhization in vitro

 The effects of sterilization time, sterilizing agents (ethanol, Chloramine T, calcium hypochlorite) and antibiotics (streptomycin and gentamycin) on Glomus mosseae (BEG 12) sporocarp germination and contamination were evaluated. Incubation for 10 s in 96 % ethanol, followed by 10 min in a solution of 2% Chloramine T, 0.02% streptomycin, 0.01% gentamycin and Tween 20, and then 6 min in 6% calcium hypochlorite greatly reduced fungal and bacterial contamination from sporocarps and caused little change in germination rate in water agar medium. Accepted: 4 March 1999