Reliability of signal transmission in stochastic nerve axon equations

We introduce a method for computing probabilities for spontaneous activity and propagation failure of the action potential in spatially extended, conductance-based neuronal models subject to noise, based on statistical properties of the membrane potential. We compare different estimators with respect to the quality of detection, computational costs and robustness and propose the integral of the membrane potential along the axon as an appropriate estimator to detect both spontaneous activity and propagation failure. Performing a model reduction we achieve a simplified analytical expression based on the linearization at the resting potential (resp. the traveling action potential). This allows to approximate the probabilities for spontaneous activity and propagation failure in terms of (classical) hitting probabilities of one-dimensional linear stochastic differential equations. The quality of the approximation with respect to the noise amplitude is discussed and illustrated with numerical results for the spatially extended Hodgkin-Huxley equations. Python simulation code is supplied on GitHub under the link https://github.com/deristnochda/Hodgkin-Huxley-SPDE.     

Population Dynamics and Damage Potential of Meloidogyne hapla to Rose Rootstock Species

The relationship between initial population densities (Pi) of Meloidogyne hapla on growth of three rose rootstocks (Rosa corymbifera ‘Laxa’, R. multiflora and R. canina ‘Inermis’) and nematode population development was studied. Each plant species was inoculated with ranges of nematode densities of 0, 0.062, 0.125, 0.25, 0.50, 1, 2, 4, 8, 16, 32, 64 and 128 second‐stage juvenile/g soil and were allowed to grow for 9 weeks. Seinhorst yield model was fitted to total fresh biomass data of the rootstocks. The tolerance limits (T) were 0.04, 0.09 and 0.01 J2/g soil and the minimum yield (m) 0.65, 0.47 and 0.43 for R. corymbifera ‘Laxa’, R. multiflora and R. canina ‘Inermis’, respectively. The reproductive factor (Pf/Pi) was highest at low initial nematode densities for all rootstocks and then decreased to below maintenance level with increasing initial population densities. Root gall severity consistently increased with initial nematode population density. Furthermore, number of root galling showed a strong positive relationship with final nematode population per gram root fresh weight. The relation between Pi and Pf was also fitted to the Seinhorst population model (Pf = (M*Pi)/Pi + M/a). Rosa multiflora supported the population of M. hapla to a maximum population density (M) of 27.53 J2/g soil with an estimated average maximum multiplication rate (a) of 24.39. For R. corymbifera ‘Laxa’ and R. canina, the maximum multiplication rate was 4.34 and 3.62 and the maximum population density 6.08 and 4.78 J2/g dry soil, respectively. Hence, it was demonstrated that all three rootstocks were susceptible to even low initial nematode densities and therefore are considered good hosts for M. hapla.     

Although there is no Physical Short‐Term Scarcity of Phosphorus,its Resource Efficiency Should be Improved

The German government has adopted a law that requires sewage plants to go beyond the recovery of phosphorus from wastewater and to promote recycling. We argue that there is no physical global short‐ or mid‐term phosphorus scarcity. However, we also argue that there are legitimate reasons for policies such as those of Germany, including: precaution as a way to ensure future generations’ long‐term supply security, promotion of technologies for closed‐loop economics in a promising stage of technology development, and decrease in the current supply risk with a new resource pool.     

Cylindrospermopsis raciborskii Virus and host: genomic characterization and ecological relevance

Cylindrospermopsis (Raphidiopsis) raciborskii is an invasive, filamentous, nitrogen-fixing cyanobacterium that forms frequent blooms in freshwater habitats. While viruses play key roles in regulating the abundance, production and diversity of their hosts in aquatic ecosystems, the role(s) of viruses in the ecology of C. raciborskii is almost unexplored. Progress in this field has been hindered by the absence of a characterized virus–host system in C. raciborskii. To bridge this gap, we sequenced the genome of CrV-01T, a previously isolated cyanosiphovirus, and its host, C. raciborskii strain Cr2010. Analyses suggest that CrV-01T represents a distinct clade of siphoviruses infecting, and perhaps lysogenizing, filamentous cyanobacteria. Its genome contains unique features that include an intact CRISPR array and a 12 kb inverted duplication. Evidence suggests CrV-01T recently gained the ability to infect Cr2010 and recently lost the ability to form lysogens. The cyanobacterial host contains a CRISPR-Cas system with CRISPR spacers matching protospacers within the inverted duplication of the CrV-01T genome. Examination of metagenomes demonstrates that viruses with high genetic identity to CrV-01T, but lacking the inverted duplication, are present in C. raciborskii blooms in Australia. The unique genomic features of the CrV/Cr2010 system offers opportunities to investigate in more detail virus–host interactions in an ecologically important bloom-forming cyanobacterium.     

Production of yoghurt with mild taste by a Lactobacillus delbrueckii subsp. bulgaricus mutant with altered proteolytic properties

In this communication, we describe the isolation of a Lactobacillus delbrueckii subsp. bulgaricus 92063 mutant strain named pH-P11, which differed from the parent strain by low proteolytic activity and altered regulation of expression of lacZ in the presence of glucose or lactose. In the presence of lactose, beta-galactosidase activity was approximately twice as high in pH-P11 than in the wild type. pH-P11 exhibited protosymbiosis together with Streptococcus thermophilus. Yoghurt produced with pH-P11 was characterized by low acidity and little post-acidification during storage. The organoleptic properties (absence of bitterness and other off-flavors, weak sourness, and clear yoghurt taste) were those of a typical "yoghurt mild". This mild flavor was achieved at rather high cell counts of lactobacilli even at the end of shelf-life. High cell counts in conjunction with high beta-galactosidase activity make pH-P11 an interesting strain for application in yoghurt especially designed for consumers with lactose malabsorption. In contrast to "yoghurt mild", which is predominantly produced with Lactobacillus acidophilus together with Streptococcus thermophilus, the product obtained by fermentation with pH-P11 and Streptococcus thermophilus concurs with international standards for yoghurt. During frequent sub-culturing, strain pH-P11, which is supposed to differ from the wild type by one or a few so-far-not-characterized mutations, showed sufficient stability for application in industrial production.     

A workflow to increase the detection rate of proteins from unsequenced organisms in high-throughput proteomics experiments

We present and evaluate a strategy for the mass spectrometric identification of proteins from organisms for which no genome sequence information is available that incorporates cross-species information from sequenced organisms. The presented method combines spectrum quality scoring, de novo sequencing and error tolerant BLAST searches and is designed to decrease input data complexity. Spectral quality scoring reduces the number of investigated mass spectra without a loss of information. Stringent quality-based selection and the combination of different de novo sequencing methods substantially increase the catalog of significant peptide alignments. The de novo sequences passing a reliability filter are subsequently submitted to error tolerant BLAST searches and MS-BLAST hits are validated by a sampling technique. With the described workflow, we identified up to 20% more groups of homologous proteins in proteome analyses with organisms whose genome is not sequenced than by state-of-the-art database searches in an Arabidopsis thaliana database. We consider the novel data analysis workflow an excellent screening method to identify those proteins that evade detection in proteomics experiments as a result of database constraints.     

Assessing enzyme activities using stable isotope labeling and mass spectrometry

Activity-based protein profiling has emerged as a valuable technology for labeling, enriching, and assessing protein activities from complex mixtures. This is primarily accomplished via a two-step identification and quantification process. Here we show a highly quantitative and streamlined method, termed catch-and-release activity profiling of enzymes (CAPE), which reduces this procedure to a single step. Furthermore the CAPE approach has the ability to detect small quantitative changes that may have been missed by alternative mass spectrometry-based techniques.     

Characterization of post-translational modifications of histone H2B-variants isolated from Arabidopsis thaliana

Eukaryotic DNA is structurally packed into chromatin by the basic histone proteins H2A, H2B, H3, and H4. There is increasing evidence that incorporation and post-translational modifications of histone variants have a fundamental role in gene regulation. While modifications of H3 and H4 histones are now well-established, considerably less is known about H2B modifications. Here, we present the first detailed characterization of H2B-variants isolated from the model plant Arabidopsis thaliana. We combined reversed-phase chromatography with tandem mass spectrometry to identify post-translational modifications of the H2B-variants HTB1, HTB2, HTB4, HTB9, and HTB11, isolated from total chromatin and euchromatin-enriched fractions. The HTB9-variant has acetylation sites at lysines 6, 11, 27, 32, 38, and 39, while Lys-145 can be ubiquitinated. Analogous modifications and an additional methylation of Lys-3 were identified for HTB11. HTB2 shows similar acetylation and ubiquitination sites and an additional methylation at Lys-11. Furthermore, the N-terminal alanine residues of HTB9 and HTB11 were found to be mono-, di-, or trimethylated or unmodified. No methylation of arginine residues was detected. The data suggest that most of these modification sites are only partially occupied. Our study significantly expands the map of covalent Arabidopsis histone modifications and is the first step to unraveling the histone code in higher plants.     

Telomere protection by mammalian Pot1 requires interaction with Tpp1

The shelterin complex at mammalian telomeres contains the single-stranded DNA-binding protein Pot1, which regulates telomere length and protects chromosome ends. Pot1 binds Tpp1, the shelterin component that connects Pot1 to the duplex telomeric DNA-binding proteins Trf1 and Trf2. Control of telomere length requires that Pot1 binds Tpp1 as well as the single-stranded telomeric DNA, but it is not known whether the protective function of Pot1 depends on Tpp1. Alternatively, Pot1 might function similarly to the Pot1-like proteins of budding and fission yeast, which have no known Tpp1-like connection to the duplex telomeric DNA. Using mutant mouse cells with diminished Tpp1 levels, RNA interference directed to mouse Tpp1 and Pot1, and complementation of mouse Pot1 knockout cells with human and mouse Pot1 variants, we show here that Tpp1 is required for the protective function of mammalian Pot1 proteins.