Determining the genetic makeup of predominant microbial taxa with specific metabolic capabilities remains one the major challenges in microbial ecology and bioprospecting due to the limitations of current cell culturing and metagenomic methods. The complexity of microbial communities and intraspecies variation hinders the assembly of individual genomes from metagenomic shotgun libraries. Here we report on the assembly and analysis of the genome of an uncultured Flavobacterium from Gulf of Maine bacterioplankton. A single cell was isolated from a coastal water sample using fluorescence-activated cell sorting. Whole genome amplification via multiple strand displacement amplification was used to prepare sufficient DNA for constructing Sanger and 454 libraries. We will discuss assembly and analysis of the single cell sequence data with an emphasis on challenges unique to this type of data, limitations of the existing method and implications for future investigations of rare and unculturable microorganisms.

© 2015, eLife Sciences Publications Ltd. All Rights Reserved.Neurons develop highly stereotyped receptive fields by coordinated growth of their dendrites. Although cell surface cues play a major role in this process, few dendrite specific signals have been

The complete genome of a model obligate methylotroph, M. flagellatus (strain KT) was sequenced. The genome is represented by a single circular chromosome of approximately 3 Mbp potentially encoding a total of 2,766 proteins. Based on genome analysis as well as the results from previous genetic and mutational analyses, methylotrophy is enabled by methanol- and methylamine dehydrogenases, the tetrahydromethanopterin-linked formaldehyde oxidation pathway, the assimilatory and dissimilatory branches of the ribulose monophosphate cycle, and a formate dehydrogenase. Some of the methylotrophy genes are present in more than one (identical or non-identical) copy. The obligate dependence on single carbon compounds is likely due to the incomplete tricarboxylic acid cycle, as no genes potentially encoding alphaketoglutarate-, malate- or succinate dehydrogenases are identifiable. The genome of M. flagellatus was compared, in terms of methylotrophy functions, to the previously sequenced genomes of three methylotrophs: Methylobacterium extorquens (Alphaproteobacterium, 7 Mbp), Methylibium petroleophilum (Betaproteobacterium, 4 Mbp), and Methylococcus capsulatus (Gammaproteobacterium, 3.3 Mbp). Strikingly, metabolically and/or phylogenetically, methylotrophy functions in M. flagellatus are more similar to the ones in M. capsulatus and M. extorquens than to the ones in the more closely related M. petroleophilum, providing the first genomic evidence of polyphyletic origin of methylotrophy in Betaproteobacteria.

Infrared fluorescent proteins (IFPs) are ideal for in vivo imaging, and monomeric versions of these proteins can be advantageous as protein tags or for sensor development. In contrast to GFP, which requires only molecular oxygen for chromophore maturation, phytochrome-derived IFPs incorporate biliverdin (BV) as the chromophore. However, BV varies in concentration in different cells and organisms. Here we engineered cells to express the haeme oxygenase responsible for BV biosynthesis and a brighter monomeric IFP mutant (IFP2.0). Together, these tools improve the imaging capabilities of IFP2.0 compared with monomeric IFP1.4 and dimeric iRFP. By targeting IFP2.0 to the plasma membrane, we demonstrate robust labelling of neuronal processes in Drosophila larvae. We also show that this strategy improves the sensitivity when imaging brain tumours in whole mice. Our work shows promise in the application of IFPs for protein labelling and in vivo imaging.

Mechanisms governing a neuron's regenerative ability are important but not well understood. We identify Rtca (RNA 3′-terminal phosphate cyclase) as an inhibitor of axon regeneration. Removal of Rtca cell-autonomously enhanced axon regrowth in the Drosophila CNS, whereas its overexpression reduced axon regeneration in the periphery. Rtca along with the RNA ligase Rtcb and its catalyst Archease operate in the RNA repair and splicing pathway important for stress-induced mRNA splicing, including that of Xbp1, a cellular stress sensor. Drosophila Rtca and Archease had opposing effects on Xbp1 splicing, and deficiency of Archease or Xbp1 impeded axon regeneration in Drosophila. Moreover, overexpressing mammalian Rtca in cultured rodent neurons reduced axonal complexity in vitro, whereas reducing its function promoted retinal ganglion cell axon regeneration after optic nerve crush in mice. Our study thus links axon regeneration to cellular stress and RNA metabolism, revealing new potential therapeutic targets for treating nervous system trauma.

Infrared fluorescent proteins (IFPs) are ideal for in vivo imaging, and monomeric versions of these proteins can be advantageous as protein tags or for sensor development. In contrast to GFP, which requires only molecular oxygen for chromophore maturation,

© 2015 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. Mechanisms governing a neuron's regenerative ability are important but not well understood. We identify Rtca (RNA 3′-terminal phosphate cyclase) as an inhibito

Alkaliphilus metalliredigens strain QYMF is an anaerobic, alkaliphilic, and metal-reducing bacterium associated with phylum Firmicutes QYMF was isolated from alkaline borax leachate ponds. The genome sequence will help elucidate the role of metal-reducing microorganisms under alkaline environments, a capability that is not commonly observed in metal respiring-microorganisms.

Riemerella anatipestifer (Hendrickson and Hilbert 1932) Segers et al. 1993 is the type species of the genus Riemerella, which belongs to the family Flavobacteriaceae. The species is of in-terest because of the position of the genus in the phylogenetic tree and because of its role as a pathogen of commercially important avian species worldwide. This is the first completed genome sequence of a member of the genus Riemerella. The 2,155,121 bp long genome with its 2,001 protein-coding and 51 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.