Green, herbicide-resistant plants by particle inflow gun-mediated gene transfer to diploid bahiagrass (Paspalum notatum)

We have established an efficient particle-bombardment transformation protocol for the diploid non-apomictic genotype of the warm season forage crop Paspalum notatum (bahiagrass). A vector containing a herbicide resistance gene (bar) together with the GUS reporter gene was used in transformation experiments. The bar gene confers resistance to the herbicide bialaphos. An improved culture system, highly regenerative callus, dense in compact polyembryogenic clusters, was produced on medium with a high CuSO4 content at elevated temperature. Target tissue (360 calli) produced under these conditions yielded 52 rooted plants on herbicide-containing medium, and 22 of these plants were PCR-positive. DNA gel blot analysis revealed a copy number of 1-5 for the GUS gene in different independent transformants. There was no correlation between copy number and GUS activity. While conventional cultures yielded exclusively albino plants on herbicide-containing medium, improved culture conditions for the target tissue resulted in the recovery of 100% green transgenic plants. All green herbicide-resistant regenerants were morphological normal and fertile.     

Mnd2, an essential antagonist of the anaphase-promoting complex during meiotic prophase

Meiotic cohesin serves in sister chromatid linkage and DNA repair until its subunit Rec8 is cleaved by separase. Separase is activated when its inhibitor, securin, is polyubiquitinated by the Cdc20 regulated anaphase-promoting complex (APC(Cdc20)) and consequently degraded. Differently regulated APCs (APC(Cdh1), APC(Ama1)) have not been implicated in securin degradation at meiosis I. We show that Mnd2, a factor known to associate with APC components, prevents premature securin degradation in meiosis by APC(Ama1). mnd2Delta cells lack linear chromosome axes and exhibit precocious sister chromatid separation, but deletion of AMA1 suppresses these defects. Besides securin, Sgo1, a protein essential for protection of centromeric cohesion during anaphase I, is also destabilized in mnd2delta cells. Mnd2's disappearance prior to anaphase II may activate APC(Ama1). Human oocytes may spend many years in meiotic prophase before maturation. Inhibitors of meiotic APC variants could prevent loss of chiasmata also in these cells, thereby guarding against aberrant chromosome segregation.     

Recombination and the origin of sequence diversity in the DRB MHC class II locus in chamois (Rupicapra spp.)

We examined the evolutionary processes contributing to genetic diversity at the major histocompatibility complex (MHC) class II DRB locus in chamois (Rupicapra spp., subfamily Caprinae). We characterised the pattern of intragenic recombination (or homologous gene conversion) and quantified the amount of recombination in the genealogical history of the two chamois species, Pyrenean chamois (Rupicapra pyrenaica) and Alpine chamois (Rupicapra rupicapra). We found evidence for intragenic recombination, and the estimated amount of population recombination suggests that recombination has been a significant process in generating DRB allelic diversity in the genealogical history of the genus Rupicapra. Moreover, positive selection appears to act on the same peptide-binding residues in both analysed chamois species, but not in identical intensity. Recombination coupled with positive selection drives the rapid evolution at the peptide-binding sites in the MHC class II DRB gene. Many chamois MHC class II DRB alleles are thus much younger than previously assumed.     

Nup155 regulates nuclear envelope and nuclear pore complex formation in nematodes and vertebrates

Nuclear envelope (NE) formation during cell division in multicellular organisms is a central yet poorly understood biological process. We report that the conserved nucleoporin Nup155 has an essential function in NE formation in Caenorhabditis elegans embryos and in Xenopus laevis egg extracts. In vivo depletion of Nup155 led to failure of nuclear lamina formation and defects in chromosome segregation at anaphase. Nup155 depletion inhibited accumulation of nucleoporins at the nuclear periphery, including those recruited to chromatin early in NE formation. Electron microscopy analysis revealed that Nup155 is also required for the formation of a continuous nuclear membrane in vivo and in vitro. Time-course experiments indicated that Nup155 is recruited to chromatin at the time of NE sealing, suggesting that nuclear pore complex assembly has to progress to a relatively late stage before NE membrane assembly occurs.     

Adeno-associated virus serotypes 1 to 5 mediated tumor cell directed gene transfer and improvement of transduction efficiency

BACKGROUND: Gene therapy is an attractive new approach for the treatment of cancer. Therefore, the development of efficient vector systems is of crucial importance in this field. Different adeno-associated virus (AAV) serotypes have been characterized so far, which show considerable differences in tissue tropism. Consequently, we aimed to characterize the most efficient serotype for this application. METHODS: To exclude all influences other than those provided by the capsid, all serotypes contained the same transgene cassette flanked by the AAV2 inverted terminal repeats. We systematically compared these vectors for efficiency in human cancer cell directed gene transfer. In order to identify limiting steps, the influence of second-strand synthesis and proteasomal degradation of AAV in a poorly transducible cell line were examined. RESULTS: AAV2 was the most efficient serotype in all solid tumor cells and primary melanoma cells with transduction rates up to 98 +/- 0.3%. Transduction above 70% could be reached with serotypes 1 (in cervical and prostate carcinoma) and 3 (in cervical, breast, prostate and colon carcinoma) using 1000 genomic particles per cell. In the colon carcinoma cell line HT-29 proteasomal degradation limited AAV1-AAV4-mediated gene transfer. Moreover, inefficient second-strand synthesis prevents AAV2-mediated transgene expression in this cell line. CONCLUSIONS: Recent advances in AAV-vector technology suggest that AAV-based vectors can be used for cancer gene therapy. Our comparative analysis revealed that, although AAV2 is the most promising candidate for such an application, serotypes 1 and 3 are valid alternatives. Furthermore, the use of self-complementary AAV vectors and proteasome inhibitors significantly improves cancer cell transduction.     

Molecular characterization, technological properties and safety aspects of enterococci from 'Hussuwa', an African fermented sorghum product

AIMS: To identify enterococci from Hussuwa, a Sudanese fermented sorghum product, and determine their technological properties and safety for possible inclusion in a starter culture preparation. METHODS AND RESULTS: Twenty-two Enterococcus isolates from Hussuwa were identified as Enterococcus faecium by using phenotypic and genotypic tests such as 16S rDNA gene sequencing, RAPD-PCR and restriction fragment length polymorphism of the 16S/23S intergenic spacer region fingerprinting. Genotyping revealed that strains were not clonally related and exhibited a considerable degree of genomic diversity. Some strains possessed useful technological properties such as production of bacteriocins and H2O2 or utilization of raffinose and stachyose. None produced alpha-amylase or tannase. A safety investigation revealed that all strains were susceptible to the antibiotics ampicillin, gentamicin, chloramphenicol, tetracycline and streptomycin, but some were resistant to ciprofloxacin, erythromycin, penicillin and vancomycin. Production of biogenic amines or presence of genes encoding virulence determinants occurred in some strains. CONCLUSIONS: Enterococcus faecium strains are associated with fermentation of Sudanese Hussuwa. Some strains exhibited useful technological properties such as production of antimicrobial agents and fermentation of indigestible sugars, which may aid in stabilizing and improving the digestibility of the product respectively. SIGNIFICANCE AND IMPACT OF THE STUDY: Enterococci were shown to play a role in the fermentation of African foods. While beneficial properties of these bacteria are indicated, their presence in this food may also imply a hygienic risk as a result of antimicrobial resistances or presence of virulence determinants.     

ALOHOMORA: a tool for linkage analysis using 10K SNP array data

SUMMARY: ALOHOMORA is a software tool designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip(R) Human Mapping 10K Array. Genotype data are converted into appropriate formats for a number of common linkage programs and subjected to standard quality control routines before linkage runs are started. ALOHOMORA is written in Perl and may be used to perform state-of-the-art linkage scans in small and large families with any genetic model. Options for using different genetic maps or ethnicity-specific allele frequencies are implemented. Graphic outputs of whole-genome multipoint LOD score values are provided for the entire dataset as well as for individual families. AVAILABILITY: ALOHOMORA is available free of charge for non-commercial research institutions. For more details, see http://gmc.mdc-berlin.de/alohomora/     

Simulation of trait- and density-mediated indirect effects induced by piscivorous predators

The study demonstrates how to use a spatially explicit individual-based model (IBM) to tackle the problem of resolving density-mediated (DMII) and trait-mediated indirect interactions (TMII) when manipulative experimentation is difficult on the scale of community-level interactions in the real word. As an example we simulated predator-induced behavioural changes in a roach (Rutilus rutilus (L.)) population before and after stocking a lake with an additional pelagic predator (Sander lucioperca (L.)). By this it was possible to calculate bioenergetic gains and costs of trait changes as well as the relative proportions of DMIIs and TMIIs in roach consumption on littoral and pelagic resources in the lake food web. Despite higher net activity costs of 64%, roach migrating horizontally over the diel cycle had a net benefit (higher energy intake of 75%) compared to roach that were restricted to the littoral as a behavioural response to the new predator. By separating the components of the indirect predator effects, we demonstrate that a predator-induced modification in prey traits (behaviour, feeding activity) could contribute substantially to the net indirect effect of a predator even when there are strong density effects. When considering the predation pressure by roach on pelagic resources, the net TMIIs due to the behavioural adaptation of the consumer in response to the predator were 13–14 times stronger than the DMIIs alone. When comparing the different effects on littoral resources it can be shown that the TMIIs approximately compensate the DMIIs thus resulting in a nearly zero net effect.

Zusammenfassung

In der vorliegenden Arbeit wurde ein räumlich explizites individuenbasiertes Modell (IBM) verwendet, um dichteabhängige (DMII) und eigenschaftsabhängige (TMII) indirekte Interaktionen zu vergleichen. Da sich dies auf der Ebene der Lebensgemeinschaft unter realen experimentellen Bedingungen als besonders schwierig erwiesen hat, wurden räuberinduzierte Verhaltensänderungen einer Plötzenpopulation (Rutilus rutilus (L.)) vor und nach dem Besatz mit einem zusätzlichen pelagischen Räuber, dem Zander (Sander lucioperca (L.)), simuliert. Dadurch war es möglich, sowohl die energetischen Kosten und Nutzen der räuberinduzierten Verhaltensänderung als auch die relativen Anteile von DMIIs and TMIIs an der Plötzenkonsumtion auf litorale und pelagische Ressourcen innerhalb des Nahrungsnetzes zu kalkulieren. Verglichen mit den Plötzen, welche sich aufgrund des neuen Räubers vor allem im Litoral aufhielten, hatten die täglich (horizontal) wandernden Plötzen trotz höherer Nettoaktivitätskosten von 64% eine größere Energieaufnahme von 75%. Durch die Auflösung der verschiedenen indirekten Räubereffekte konnten wir demonstrieren, dass räuberinduzierte Modifikationen von Beuteeigenschaften (Verhalten, Fraßaktivität) erheblich zu den indirekten Nettoeffekten eines Räubers beitragen können, auch wenn starke dichteabhängige Effekte vorhanden sind. Wenn man die Plötzenkonsumtion auf pelagische Ressourcen betrachtet, so ergeben sich 13-14 fach stärkere TMIIs als DMIIs. Wenn man die verschiedenen Effekte auf litorale Ressourcen vergleicht, zeigt es sich, dass TMIIs die DMIIs kompensieren, wodurch der indirekte Nettoeffekt fast null beträgt.     

Calculating the evolutionary rates of different genes: a fast, accurate estimator with applications to maximum likelihood phylogenetic analysis

In phylogenetic analyses with combined multigene or multiprotein data sets, accounting for differing evolutionary dynamics at different loci is essential for accurate tree prediction. Existing maximum likelihood (ML) and Bayesian approaches are computationally intensive. We present an alternative approach that is orders of magnitude faster. The method, Distance Rates (DistR), estimates rates based upon distances derived from gene/protein sequence data. Simulation studies indicate that this technique is accurate compared with other methods and robust to missing sequence data. The DistR method was applied to a fungal mitochondrial data set, and the rate estimates compared well to those obtained using existing ML and Bayesian approaches. Inclusion of the protein rates estimated from the DistR method into the ML calculation of trees as a branch length multiplier resulted in a significantly improved fit as measured by the Akaike Information Criterion (AIC). Furthermore, bootstrap support for the ML topology was significantly greater when protein rates were used, and some evident errors in the concatenated ML tree topology (i.e., without protein rates) were corrected. [Bayesian credible intervals; DistR method; multigene phylogeny; PHYML; rate heterogeneity.].     

A novel assay of cell rubidium uptake using graphite furnace atomic absorption: application to rats on a magnesium-deficient diet

The [Na,K]ATPase or sodium pump (SP) is a ubiquitous membrane cation transport system. Because of its potential participation in the pathophysiology of essential hypertension and cataract formation, the SP is under active investigation to detail its function and control. In this paper, we describe a novel, nonradioactive method of measuring SP ion transport activity in intact red blood cells (RBCs) using graphite furnace atomic absorption measurement of rubidium ion (Rb) uptake. This method provided sensitivity comparable to radioactive techniques, as assessed by experiments with human red blood cells (RBC) and ouabain, a known SP inhibitor, but this analytical approach eliminates the use of radioisotopes common to other Rb uptake assay methods. As a demonstration of its broader utility, the assay was used to assess the effects of dietary magnesium intake on SP-mediated ion transport in the RBCs of diet-controlled rats. Rats on 7 weeks of a magnesium-deficient (MgD) diet showed significant reductions in serum magnesium concentration, although levels remained in the lower region of the reference interval for healthy, magnesium replete animals. Red cell Rb uptake was significantly reduced in cells from the magnesium-restricted animals, demonstrating the sensitivity of Rb uptake to reduced magnesium intake, despite serum levels that fell within the reported normal range, and the utility of this Rb uptake assay in measuring physiological changes in SP function.