Non-Mendelian Mutation Allowing Ureidosuccinic Acid Uptake in Yeast

Mutants of Saccharomyces cerevisiae capable of growth on a minimal medium supplemented with ureidosuccinic and glutamic acids have been isolated from a pyrimidineless strain. One of these mutants consistently yielded a non-Mendelian meiotic segregation. Moreover, the mitotic transmission of the mutation was very high. It is suggested that the mutation is nonchromosomal and could be mitochondrial. However, this mutation behaves very differently from other mitochondrial mutations.     

Self-pollination,style length development and seed set in self-compatible Asteraceae: evidence from Senecio vulgaris L.

Background: Variation in style length has been reported in Senecio vulgaris and has been associated with outcrossing rate.

Aims: To determine if (i) long styles lack germinated pollen on stigmas left to self-pollinate, (ii) successful self-pollination causes styles to stop elongating and shrink in length and (iii) seed set increases with the amount of pollen deposited on stigmas.

Methods: Determined germinated self-pollen on stigmas of long and short styles after auto-self-pollination; scored style length over 48 h in self-pollinated and non-pollinated florets; recorded seed set after placing different amounts of pollen on stigmas.

Results: Most long-styled florets had zero or low amounts of germinated pollen on stigmas in contrast to most short-styled florets. Styles initially elongated to the same length in self-pollinated and non-pollinated florets, then shrank in length in self-pollinated florets while continuing to elongate in non-pollinated florets. Seed set increased with number of pollen grains deposited on stigmas.

Conclusions: Successful self-pollen deposition and/or germination on stigmas of S. vulgaris are indicated by presence of short styles, whereas the opposite is indicated by presence of long styles in florets left to self-pollinate. Self-pollination causes styles to shrink after initially elongating. Seed set is dependent on the amount of pollen deposited on stigmas.     

Conserving a variety of ancient forest patches maintains historic arthropod diversity

Forests are naturally extensive tracts. However, in South Africa natural fires over many millennia have reduced forested areas into small remnants spread throughout a grassland matrix. Small patches, especially distant patches, are generally considered to be adverse for forest specialists, owing to decreased forest interior and increased edge. Here we test this assumption by determining the impact of forest interpatch distance and patch size on epigaeic arthropod diversity in this globally rare vegetation type. Forty patches were selected: ten large (100–435 m diameter) that are distant (500–645 m) from other patches, ten large that are close to other patches (38–97 m), ten small (30–42 m) that are distant, and ten small-close patches. Each patch had two plots: edge and interior. Arthropods were sampled using pitfall traps, Berlese-Tullgren funnels and active searches. Interiors and edges had similar species richness and composition, excluding spiders, which were richer in interiors. Patch size significantly influenced species richness of predatory beetles and arthropod assemblages, excluding spiders. Effect of the interaction between patch size and interpatch distance on species richness and composition varied among taxa. Furthermore, large patches supported similar assemblages regardless of interpatch distance. Arthropod response, particularly ants to patch size and interpatch distance, was partly shaped by the matrix type. The percentage of surrounding grassland had little effect on arthropod diversity. We can conclude that large and close patches are important for arthropod conservation. Nevertheless, it is also important to conserve a variety of patch sizes at various distances to maximize overall arthropod composition.     

Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers

Many microbial communities are characterized by high genetic diversity. 16S ribosomal RNA sequencing can determine community members, and metagenomics can determine the functional diversity, but resolving the functional role of individual cells in high throughput remains an unsolved challenge. Here, we describe epicPCR (Emulsion, Paired Isolation and Concatenation PCR), a new technique that links functional genes and phylogenetic markers in uncultured single cells, providing a throughput of hundreds of thousands of cells with costs comparable to one genomic library preparation. We demonstrate the utility of our technique in a natural environment by profiling a sulfate-reducing community in a freshwater lake, revealing both known sulfate reducers and discovering new putative sulfate reducers. Our method is adaptable to any conserved genetic trait and translates genetic associations from diverse microbial samples into a sequencing library that answers targeted ecological questions. Potential applications include identifying functional community members, tracing horizontal gene transfer networks and mapping ecological interactions between microbial cells.     

Polyploid formation via chromosome duplication induced by CTP:phosphocholine cytidylyltransferase deficiency and Bcl-2 overexpression: identification of two novel endogenous factors.

Polyploidy is a profound phenotype found in tumors and its mechanism is unknown. We report here that when B-cell lymphoma gene-2 (Bcl-2) was overexpressed in a Chinese hamster ovary cell line that was deficient in CTP:phosphocholine cytidylyltransferase (CT), cellular DNA content doubled. The higher DNA content was due to a permanent conversion from diploid cells to tetraploid cells. The mechanism of polyploid formation could be attributed to the duplication of 18 parental chromosomes. The rate of conversion from diploid to tetraploid was Bcl-2 dose dependent. The diploid genome was not affected by Bcl-2 expression or by CT deficiency alone. Endogenous CT or expression of recombinant rat liver CTalpha prior to Bcl-2 expression prevented the formation of polyploid cells. This conversion was irreversible even when both initiating factors were removed. In this study, we have identified Bcl-2 as a positive regulator and CTalpha as a negative regulator of polyploid formation.     

Maternal transmission of SIVsmm in rhesus macaques

Fifteen SIV-infected rhesus monkeys delivered 13 livebirths and two stillbirths; one livebirth died at three days of age. While all infants were culture-negative for SIV at birth, nine had maternal antibodies that disappeared by six months of age. Three infants subsequently seroconverted and became virus positive at 9–15 months. Milk samples from all mothers were virus-negative at parturition but samples from four animals were virus-positive at nine and 12 months. This study documents maternal transmission of SIV and suggests transmission by breast-feeding.     

Leaf growth rate per unit thermal time follows QTL-dependent daily patterns in hundreds of maize lines under naturally fluctuating conditions

We have analysed daily patterns of leaf elongation rate (LER) in large data sets with 318 genotypes placed in naturally fluctuating temperature and evaporative demand, and examined the effect of targeted alleles on these patterns. The method consisted, firstly, in expressing elongation rate per unit thermal time, so it became temperature independent; secondly, in a joint analysis of diurnal fluctuations of elongation rate and of micrometeorological conditions in several experiments, and finally, in a comparison of daily patterns between groups of genotypes possessing targeted alleles. (1) Conditions for using thermal time at a time step of 15 min were first tested successfully in 318 recombinant inbred lines (RILs) of three mapping populations. (2) An analysis of 1989 time courses revealed a robust daily pattern of LER per unit thermal time (LERth) over several experiments. LERth was constant during the night and was reproducible (for a given RIL) over up to 10 consecutive nights in different experiments. It declined rapidly during the early morning, closely following the daily pattern of transpiration rate. (3) Groups of RILs carrying alleles conferring a high response to temperature had markedly higher night-time plateau of LER than those with low responses. Groups of RILs with high response to evaporative demand had rapid decreases in elongation rate at the transition between night and day, while this decrease was slower in groups of RILs with low response. These results open the way for using kinetics of responses to environmental stimuli as a phenotyping tool in genetic analyses.     

Predicted effects of missense mutations on native-state stability account for phenotypic outcome in phenylketonuria, a paradigm of misfolding diseases

Phenylketonuria (PKU) is a genetic disease caused by mutations in human phenylalanine hydroxylase (PAH). Most missense mutations result in misfolding of PAH, increased protein turnover, and a loss of enzymatic function. We studied the prediction of the energetic impact on PAH native-state stability of 318 PKU-associated missense mutations, using the protein-design algorithm FoldX. For the 80 mutations for which expression analyses have been performed in eukaryote systems, in most cases we found substantial overall correlations between the mutational energetic impact and both in vitro residual activities and patient metabolic phenotype. This finding confirmed that the decrease in protein stability is the main molecular pathogenic mechanism in PKU and the determinant for phenotypic outcome. Metabolic phenotypes have been shown to be better predicted than in vitro residual activities, probably because of greater stringency in the phenotyping process. Finally, all the remaining 238 PKU missense mutations compiled at the PAH locus knowledgebase (PAHdb) were analyzed, and their phenotypic outcomes were predicted on the basis of the energetic impact provided by FoldX. Residues in exons 7-9 and in interdomain regions within the subunit appear to play an important structural role and constitute hotspots for destabilization. FoldX analysis will be useful for predicting the phenotype associated with rare or new mutations detected in patients with PKU. However, additional factors must be considered that may contribute to the patient phenotype, such as possible effects on catalysis and interindividual differences in physiological and metabolic processes.     

Classification methods for ongoing EEG and MEG signals

Classification algorithms help predict the qualitative properties of a subject's mental state by extracting useful information from the highly multivariate non-invasive recordings of his brain activity. In particular, applying them to Magneto-encephalography (MEG) and electro-encephalography (EEG) is a challenging and promising task with prominent practical applications to e.g. Brain Computer Interface (BCI). In this paper, we first review the principles of the major classification techniques and discuss their application to MEG and EEG data classification. Next, we investigate the behavior of classification methods using real data recorded during a MEG visuomotor experiment. In particular, we study the influence of the classification algorithm, of the quantitative functional variables used in this classifier, and of the validation method. In addition, our findings suggest that by investigating the distribution of classifier coefficients, it is possible to infer knowledge and construct functional interpretations of the underlying neural mechanisms of the performed tasks. Finally, the promising results reported here (up to 97% classification accuracy on 1-second time windows) reflect the considerable potential of MEG for the continuous classification of mental states.