Systematic identification of gene families for use as markers for phylogenetic and phylogeny- driven ecological studies of bacteria and archaea and their major subgroups

With the astonishing rate that the genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families that are particularly well suited for the tasks at hand. Such gene families have generally been referred to as marker genes. We are particularly interested in identifying and using such marker genes for phylogenetic and phylogeny-driven ecological studies of microbes and their communities. We therefore refer to these as PhyEco (for phylogenetic and phylogenetic ecology) markers. The dual use of these PhyEco markers means that we needed to develop and apply a set of somewhat novel criteria for identification of the best candidates for such markers. The criteria we focused on included universality across the taxa of interest, ability to be used to produce robust phylogenetic trees that reflect as much as possible the evolution of the species from which the genes come, and low variation in copy number across taxa. We describe here an automated protocol for identifying potential PhyEco markers from a set of complete genome sequences. The protocol combines rapid searching, clustering and phylogenetic tree building algorithms to generate protein families that meet the criteria listed above. We report here the identification of PhyEco markers for different taxonomic levels including 40 for all bacteria and archaea, 114 for all bacteria, and much more for some of the individual phyla of bacteria. This new list of PhyEco markers should allow much more detailed automated phylogenetic and phylogenetic ecology analyses of these groups than possible previously.Comment: 24 pages, 3 figure

Whole genome sequence analysis reveals the broad distribution of the RtxA type 1 secretion system and four novel putative type 1 secretion systems throughout the Legionella genus.

Type 1 secretion systems (T1SSs) are broadly distributed among bacteria and translocate effectors with diverse function across the bacterial cell membrane. Legionella pneumophila, the species most commonly associated with Legionellosis, encodes a T1SS at the lssXYZABD locus which is responsible for the secretion of the virulence factor RtxA. Many investigations have failed to detect lssD, the gene encoding the membrane fusion protein of the RtxA T1SS, in non-pneumophila Legionella, which has led to the assumption that this system is a virulence factor exclusively possessed by L. pneumophila. Here we discovered RtxA and its associated T1SS in a novel Legionella taurinensis strain, leading us to question whether this system may be more widespread than previously thought. Through a bioinformatic analysis of publicly available data, we classified and determined the distribution of four T1SSs including the RtxA T1SS and four novel T1SSs among diverse Legionella spp. The ABC transporter of the novel Legionella T1SS Legionella repeat protein secretion system shares structural similarity to those of diverse T1SS families, including the alkaline protease T1SS in Pseudomonas aeruginosa. The Legionella bacteriocin (1-3) secretion systems T1SSs are novel putative bacteriocin transporting T1SSs as their ABC transporters include C-39 peptidase domains in their N-terminal regions, with LB2SS and LB3SS likely constituting a nitrile hydratase leader peptide transport T1SSs. The LB1SS is more closely related to the colicin V T1SS in Escherichia coli. Of 45 Legionella spp. whole genomes examined, 19 (42%) were determined to possess lssB and lssD homologs. Of these 19, only 7 (37%) are known pathogens. There was no difference in the proportions of disease associated and non-disease associated species that possessed the RtxA T1SS (p = 0.4), contrary to the current consensus regarding the RtxA T1SS. These results draw into question the nature of RtxA and its T1SS as a singular virulence factor. Future studies should investigate mechanistic explanations for the association of RtxA with virulence

Particle trajectory tracing for electrostatic and magnetostatic fields

This work reports a numerical method for single charged particle trajectories computation in 2D electrostatic and magnetostatic stationary fields, in other words, fields that do not change in time. This is approached by the finite element method domain discretisation, and numerical computation of particle trajectory, calculated by the two step centred in time method, which calculates the particle position on the next step using a dummy step in order to increase the accuracy for the same step size. Given particle's coordinates, the finite element that contains that particle is found based on Lohner's algorithm. The examples used to test the method are a electric deflector for the electric case and cyclotron for the magnetic case. Both are very important devices to science and technology, being used in a variety of domestic and industrial appliances and in several scientific and technologic researches. Other particle optics devices can benefit of the method proposed in this paper, as beam bending devices and spectrometers, among others. This method can be easily extended for particle trajectories computation in 3D domains, can be extended also for dynamic fields and for the relativistic case, which is ideal for the typical speed involved when working with particles near the atomic level

Peranan Orang Tua dalam Mengatasi Kenakalan Remaja Akibat Meminum Alkhohol Cap Tikus (Studi Kasus di Desa Talawaan Kecamatan Talawaan Kabupaten Minahasa Utara)”

Kids Teens who commit crimes were generally lacking self-control, or the control ofabusing themselves instead, and likes to enforce its own rules without regard to the presence of others in thevicinity. The incidence of such behaviour can also be caused by factors in socialization; they often hang outwith friends without looking at his background. And in general, these children very selfish, and likesto abuse or even exaggerate the price themselves. On the basis of a sense of glad they did it without regardto the effects that will be accepted. In rural areas, many acts of juvenile delinquency are very differentwith that occurs in urban areas, one of the causes of juvenile delinquency in rural areas is the drinking ofliquor among other drinks which high levels of alcohol such as the rat Stamp. Based on the backgroundof the issue that became a goal in this research is to know the role of parents in addressing the rateof juvenile delinquency as a result of the rat Stamp liquor in the village of Talawaan.The methods used in this research is qualitative research methods. In this study to understand aphenomenon in social context by nature with emphasis on the process ofdeep communication interaction between researchers with the phenomena examined. Techniquesof collection and processing of data in the research carried out in the form,namely: Observation/observation. Interview. Primary data and secondary data, the study documents.Results of the study prove that the forms of delinquency are experienced by teens affected by lackof parental control, the influence of the environment both in the school environment aswell as social environments, as well as the impact of globalization, among others, the influence of the massmedia such as television, Computer Media, and others. Results of the study prove that the forms of juveniledelinquency are extremely diverse and complex, where the offences and crimes committedby teenagers have already violated the rules and values of decency that occurred in the community suchas violating legal norms and customs

The political economy of the Jospin government

This article explores the political economy of the French Socialist Party (PS), beginning with the neo-liberal U-turn of 1983. It then charts the re-evaluation of the PS's political economic foundations after the 1993 defeat, the rejection of the neo-liberal 'pensée unique', and the rehabilitation of a broadly Keynesian frame of reference. The article goes on to explore how this shift has fed through into the Jospin government's policy and positions at both the national and international level. It explores aspirations to reinvent the EU as a Keynesian social democratic 'policy space', and at the national level, employment, macroeconomic, and structural policies

Global marine bacterial diversity peaks at high latitudes in winter.

Genomic approaches to characterizing bacterial communities are revealing significant differences in diversity and composition between environments. But bacterial distributions have not been mapped at a global scale. Although current community surveys are way too sparse to map global diversity patterns directly, there is now sufficient data to fit accurate models of how bacterial distributions vary across different environments and to make global scale maps from these models. We apply this approach to map the global distributions of bacteria in marine surface waters. Our spatially and temporally explicit predictions suggest that bacterial diversity peaks in temperate latitudes across the world's oceans. These global peaks are seasonal, occurring 6 months apart in the two hemispheres, in the boreal and austral winters. This pattern is quite different from the tropical, seasonally consistent diversity patterns observed for most macroorganisms. However, like other marine organisms, surface water bacteria are particularly diverse in regions of high human environmental impacts on the oceans. Our maps provide the first picture of bacterial distributions at a global scale and suggest important differences between the diversity patterns of bacteria compared with other organisms

Hands-on Bayesian Neural Networks -- a Tutorial for Deep Learning Users

Modern deep learning methods constitute incredibly powerful tools to tackle a myriad of challenging problems. However, since deep learning methods operate as black boxes, the uncertainty associated with their predictions is often challenging to quantify. Bayesian statistics offer a formalism to understand and quantify the uncertainty associated with deep neural network predictions. This tutorial provides an overview of the relevant literature and a complete toolset to design, implement, train, use and evaluate Bayesian Neural Networks, i.e. Stochastic Artificial Neural Networks trained using Bayesian methods.Comment: 35 pages, 15 figure