Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2

Placozoa is an enigmatic phylum of simple, microscopic, marine metazoans(1,2). Although intracellular bacteria have been found in all members of this phylum, almost nothing is known about their identity, location and interactions with their host(3-6). We used metagenomic and metatranscriptomic sequencing of single host individuals, plus metaproteomic and imaging analyses, to show that the placozoan Trichoplax sp. H2 lives in symbiosis with two intracellular bacteria. One symbiont forms an undescribed genus in the Midichloriaceae (Rickettsiales)(7,8) and has a genomic repertoire similar to that of rickettsial parasites(9,10), but does not seem to express key genes for energy parasitism. Correlative image analyses and three-dimensional electron tomography revealed that this symbiont resides in the rough endoplasmic reticulum of its host's internal fibre cells. The second symbiont belongs to the Margulisbacteria, a phylum without cultured representatives and not known to form intracellular associations(11-13). This symbiont lives in the ventral epithelial cells of Trichoplax, probably metabolizes algal lipids digested by its host and has the capacity to supplement the placozoan's nutrition. Our study shows that one of the simplest animals has evolved highly specific and intimate associations with symbiotic, intracellular bacteria and highlights that symbioses can provide access to otherwise elusive microbial dark matter

Paracatenula, an ancient symbiosis between thiotrophic Alphaproteobacteria and catenulid flatworms

Harnessing chemosynthetic symbionts is a recurring evolutionary strategy. Eukaryotes from six phyla as well as one archaeon have acquired chemoautotrophic sulfur-oxidizing bacteria. In contrast to this broad host diversity, known bacterial partners apparently belong to two classes of bacteria—the Gamma- and Epsilonproteobacteria. Here, we characterize the intracellular endosymbionts of the mouthless catenulid flatworm genus Paracatenula as chemoautotrophic sulfur-oxidizing Alphaproteobacteria. The symbionts of Paracatenula galateia are provisionally classified as “Candidatus Riegeria galateiae” based on 16S ribosomal RNA sequencing confirmed by fluorescence in situ hybridization together with functional gene and sulfur metabolite evidence. 16S rRNA gene phylogenetic analysis shows that all 16 Paracatenula species examined harbor host species-specific intracellular Candidatus Riegeria bacteria that form a monophyletic group within the order Rhodospirillales. Comparing host and symbiont phylogenies reveals strict cocladogenesis and points to vertical transmission of the symbionts. Between 33% and 50% of the body volume of the various worm species is composed of bacterial symbionts, by far the highest proportion among all known endosymbiotic associations between bacteria and metazoans. This symbiosis, which likely originated more than 500 Mya during the early evolution of flatworms, is the oldest known animal–chemoautotrophic bacteria association. The distant phylogenetic position of the symbionts compared with other mutualistic or parasitic Alphaproteobacteria promises to illuminate the common genetic predispositions that have allowed several members of this class to successfully colonize eukaryote cells

New consistency index based on inertial operating speed

The occurrence of road crashes depends on several factors, with design consistency (i.e., conformance of highway geometry to drivers' expectations) being one of the most important. A new consistency model for evaluating the performance of tangent-to-curve transitions on two-lane rural roads was developed. This model was based on the inertial consistency index (ICI) defined for each transition. The ICI was calculated at the beginning point of the curve as the difference between the average operating speed on the previous 1-km road segment (inertial operating speed) and the actual operating speed at this point. For the calibration of the ICI and its thresholds, 88 road segments, which included 1,686 tangent-to-curve transitions, were studied. The relationship between those results and the crash rate associated with each transition was analyzed. The results showed that the higher the ICI was, the higher the crash rate; thus, the probability of accidents increased. Similar results were obtained from the study of the relationship between the ICI and the weighted average crash rate of the corresponding group of transitions. A graphical and statistical analysis established that road consistency might be considered good when the ICI was lower than 10 km/h, poor when the ICI was higher than 20 km/h, and fair otherwise. A validation process that considered 20 road segments was performed. The ICI values obtained were highly correlated to the number of crashes that had occurred at the analyzed transitions. Thus, the ICI and its consistency thresholds resulted in a new approach for evaluation of consistency.The authors thank the Center for Studies and Experimentation of Public Works of the Spanish Ministry of Public Works, which partially subsidized the data collection, for obtaining the empirical operating speed profiles used in the validation process. The authors also thank the General Directorate of Public Works of the Infrastructure and Transportation Department of the Valencian government, the Valencian Province Council, and the General Directorate of Traffic of the Ministry of the Interior of the Government of Spain for their cooperation in data gathering.García García, A.; Llopis Castelló, D.; Camacho Torregrosa, FJ.; Pérez Zuriaga, AM. (2013). New consistency index based on inertial operating speed. Transportation Research Record. (2391):105-112. doi:10.3141/2391-10S1051122391Ng, J. C. ., & Sayed, T. (2004). Effect of geometric design consistency on road safety. Canadian Journal of Civil Engineering, 31(2), 218-227. doi:10.1139/l03-090Gibreel, G. M., Easa, S. M., Hassan, Y., & El-Dimeery, I. A. (1999). State of the Art of Highway Geometric Design Consistency. Journal of Transportation Engineering, 125(4), 305-313. doi:10.1061/(asce)0733-947x(1999)125:4(305)Hassan, Y. (2004). Highway Design Consistency: Refining the State of Knowledge and Practice. Transportation Research Record: Journal of the Transportation Research Board, 1881(1), 63-71. doi:10.3141/1881-08Polus, A., & Mattar-Habib, C. (2004). New Consistency Model for Rural Highways and Its Relationship to Safety. Journal of Transportation Engineering, 130(3), 286-293. doi:10.1061/(asce)0733-947x(2004)130:3(286)Cafiso, S., Di Graziano, A., Di Silvestro, G., La Cava, G., & Persaud, B. (2010). Development of comprehensive accident models for two-lane rural highways using exposure, geometry, consistency and context variables. Accident Analysis & Prevention, 42(4), 1072-1079. doi:10.1016/j.aap.2009.12.015Zuriaga, A. M. P., García, A. G., Torregrosa, F. J. C., & D’Attoma, P. (2010). Modeling Operating Speed and Deceleration on Two-Lane Rural Roads with Global Positioning System Data. Transportation Research Record: Journal of the Transportation Research Board, 2171(1), 11-20. doi:10.3141/2171-0

Biostimulantien als Blattapplikation wirken auf Spross- und Wurzelmasse sowie Wurzelaktivität in Ackerbohnen (Vicia Faba)

Topfversuch wurde die Wirkung von Biostimulanzien auf die Wurzel- und Sprossparameter der Ackerbohne untersucht. Komposttee und sterilisierter Komposttee erhöhten die Trockensubstanz der Wurzel- und Sprossmasse signifikant. Lithokraft® erhöhte das Gewicht der Rhizosheath und der Knöllchen

Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria).

Assie A, Leisch N, Meier DV, et al. Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria). The ISME journal. 2019;14(1):104-122.Most autotrophs use the Calvin-Benson-Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts ("Candidatus Thiobarba") of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cyclegenes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that "Ca. Thiobarba" switched from the rTCA cycle to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated "Ca. Thiobarba". Direct stable isotope fingerprinting showed that "Ca. Thiobarba" has typical CBB signatures, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment

Spray Deposition of High Quality CuInSe2 and CdTe Films: Preprint

A number of different ink and deposition approaches have been used for the deposition of CuInSe2 (CIS), Cu(In,Ga)Se2 (CIGS), and CdTe films. For CIS and CIGS, soluble precursors containing Cu, In, and Ga have been developed and used in two ways to produce CIS films. In the first, In-containing precursor films were sprayed on Mo-coated glass substrates and converted by rapid thermal processing (RTP) to In2Se3. Then a Cu-containing film was sprayed down on top of the In2Se3 and the stacked films were again thermally processed to give CIS. In the second approach, the Cu-, In-, and Ga-containing inks were combined in the proper ratio to produce a mixed Cu-In-Ga ink that was sprayed on substrates and thermally processed to give CIGS films directly. For CdTe deposition, ink consisting of CdTe nanoparticles dispersed in methanol was prepared and used to spray precursor films. Annealing these precursor films in the presence of CdCl2 produced large-grained CdTe films. The films were characterized by x-ray diffraction (XRD) and scanning electron microscopy (SEM). Optimized spray and processing conditions are crucial to obtain dense, crystalline films

New geometric design consistency model based on operating speed profiles for road safety evaluation

[EN] To assist in the on-going effort to reduce road fatalities as much as possible, this paper presents a new methodology to evaluate road safety in both the design and redesign stages of two-lane rural highways. This methodology is based on the analysis of road geometric design consistency, a value which will be a surrogate measure of the safety level of the two-lane rural road segment. The consistency model presented in this paper is based on the consideration of continuous operating speed profiles. The models used for their construction were obtained by using an innovative GPS-data collection method that is based on continuous operating speed profiles recorded from individual drivers. This new methodology allowed the researchers to observe the actual behavior of drivers and to develop more accurate operating speed models than was previously possible with spot-speed data collection, thereby enabling a more accurate approximation to the real phenomenon and thus a better consistency measurement. Operating speed profiles were built for 33 Spanish two-lane rural road segments, and several consistency measurements based on the global and local operating speed were checked. The final consistency model takes into account not only the global dispersion of the operating speed, but also some indexes that consider both local speed decelerations and speeds over posted speeds as well. For the development of the consistency model, the crash frequency for each study site was considered, which allowed estimating the number of crashes on a road segment by means of the calculation of its geometric design consistency. Consequently, the presented consistency evaluation method is a promising innovative tool that can be used as a surrogate measure to estimate the safety of a road segment.The authors would like to thank the Center for Studies and Experimentation of Public Works (CEDEX) of the Spanish Ministry of PublicWorks for partially subsidizing this research.We also wish to thank the Infrastructure and Transportation Department of the General Directorate of Public Works of the Valencian Government, to the Valencian Provincial Council, and to the Ministry of the Interior, especially the General Directorate of Traffic of Spain, for their cooperation in field data gathering.Camacho Torregrosa, FJ.; Pérez Zuriaga, AM.; Campoy Ungria, JM.; García García, A. (2013). New geometric design consistency model based on operating speed profiles for road safety evaluation. Accident Analysis and Prevention. 61:33-42. doi:10.1016/j.aap.2012.10.001S33426

The Substrate-Bound Crystal Structure of a Baeyer–Villiger Monooxygenase Exhibits a Criegee-like Conformation

The Baeyer\u2013Villiger monooxygenases (BVMOs) are a family of bacterial flavoproteins that catalyze the synthetically useful Baeyer\u2013Villiger oxidation reaction. This involves the conversion of ketones into esters or cyclic ketones into lactones by introducing an oxygen atom adjacent to the carbonyl group. The BVMOs offer exquisite regio- and enantiospecificity while acting on a wide range of substrates. They use only NADPH and oxygen as cosubstrates, and produce only NADP+ and water as byproducts, making them environmentally attractive for industrial purposes. Here, we report the first crystal structure of a BVMO, cyclohexanone monooxygenase (CHMO) from Rhodococcus sp. HI-31 in complex with its substrate, cyclohexanone, as well as NADP+ and FAD, to 2.4 \uc5 resolution. This structure shows a drastic rotation of the NADP+ cofactor in comparison to previously reported NADP+-bound structures, as the nicotinamide moiety is no longer positioned above the flavin ring. Instead, the substrate, cyclohexanone, is found at this location, in an appropriate position for the formation of the Criegee intermediate. The rotation of NADP+ permits the substrate to gain access to the reactive flavin peroxyanion intermediate while preventing it from diffusing out of the active site. The structure thus reveals the conformation of the enzyme during the key catalytic step. CHMO is proposed to undergo a series of conformational changes to gradually move the substrate from the solvent, via binding in a solvent excluded pocket that dictates the enzyme\u2019s chemospecificity, to a location above the flavin\u2013peroxide adduct where catalysis occurs.Peer reviewed: YesNRC publication: Ye

The Sloan Great Wall. Rich clusters

We present the results of the study of the substructure and galaxy content of ten rich clusters of galaxies in three different superclusters of the Sloan Great Wall. We determine the substructure in clusters using the 'Mclust' package from the 'R' statistical environment and analyse their galaxy content. We analyse the distribution of the peculiar velocities of galaxies in clusters and calculate the peculiar velocity of the first ranked galaxy. We show that clusters in our sample have more than one component; in some clusters different components also have different galaxy content. We find that in some clusters with substructure the peculiar velocities of the first ranked galaxies are large. All clusters in our sample host luminous red galaxies. They can be found both in the central areas of clusters as well as in the outskirts, some of them have large peculiar velocities. About 1/3 of red galaxies in clusters are spirals. The scatter of colours of red ellipticals is in most clusters larger than that of red spirals. The presence of substructure in rich clusters, signs of possible mergers and infall, as well as the large peculiar velocities of the first ranked galaxies suggest that the clusters in our sample are not yet virialized. We present merger trees of dark matter haloes in an N-body simulation to demonstrate the formation of present-day dark matter haloes via multiple mergers during their evolution. In simulated dark matter haloes we find a substructure similar to that in observed clusters.Comment: 19 pages, 44 figures, accepted for publication in Astronomy and Astrophysic

Statistical analysis and significance testing of serial analysis of gene expression data using a Poisson mixture model

<p>Abstract</p> <p>Background</p> <p>Serial analysis of gene expression (SAGE) is used to obtain quantitative snapshots of the transcriptome. These profiles are count-based and are assumed to follow a Binomial or Poisson distribution. However, tag counts observed across multiple libraries (for example, one or more groups of biological replicates) have additional variance that cannot be accommodated by this assumption alone. Several models have been proposed to account for this effect, all of which utilize a continuous prior distribution to explain the excess variance. Here, a Poisson mixture model, which assumes excess variability arises from sampling a mixture of distinct components, is proposed and the merits of this model are discussed and evaluated.</p> <p>Results</p> <p>The goodness of fit of the Poisson mixture model on 15 sets of biological SAGE replicates is compared to the previously proposed hierarchical gamma-Poisson (negative binomial) model, and a substantial improvement is seen. In further support of the mixture model, there is observed: 1) an increase in the number of mixture components needed to fit the expression of tags representing more than one transcript; and 2) a tendency for components to cluster libraries into the same groups. A confidence score is presented that can identify tags that are differentially expressed between groups of SAGE libraries. Several examples where this test outperforms those previously proposed are highlighted.</p> <p>Conclusion</p> <p>The Poisson mixture model performs well as a) a method to represent SAGE data from biological replicates, and b) a basis to assign significance when testing for differential expression between multiple groups of replicates. Code for the R statistical software package is included to assist investigators in applying this model to their own data.</p