Most methods to culture cells in three dimensions depend on a cell-seedable biomaterial to define the global structure of the culture and the microenvironment of the cells. Efforts to tailor these scaffolds have focused on the chemical and mechanical properties of the biomaterial itself. Here, we present a strategy to control the distributions of soluble chemicals within the scaffold with convective mass transfer via microfluidic networks embedded directly within the cell-seeded biomaterial. Our presentation of this strategy includes: a lithographic technique to build functional microfluidic structures within a calcium alginate hydrogel seeded with cells; characterization of this process with respect to microstructural fidelity and cell viability; characterization of convective and diffusive mass transfer of small and large solutes within this microfluidic scaffold; and demonstration of temporal and spatial control of the distribution of non-reactive solutes and reactive solutes (that is, metabolites) within the bulk of the scaffold. This approach to control the chemical environment on a micrometre scale within a macroscopic scaffold could aid in engineering complex tissues.

Methylobacter tundripaludum SV96T (ATCC BAA-1195) is a psychrotolerant aerobic methane-oxidizing gammaproteobacterium (Methylococcales, Methylococcaceae) living in High Arctic wetland soil. The strain was isolated from soil harvested in July 1996 close to the settlement Ny-Ålesund, Svalbard, Norway (78°56N, 11°53E), and described as a novel species in 2006. The genome includes pmo and pxm operons encoding copper membrane monooxygenases (Cu-MMOs), genes required for nitrogen fixation, and the nirS gene implicated in dissimilatory nitrite reduction to NO but no identifiable inventory for further processing of nitrogen oxides. These genome data provide the basis to investigate M. tundripaludum SV96, identified as a major player in the biogeochemistry of Arctic environments.Arctic permafrost environments are methane (CH 4 ) reservoirs. Ongoing and future changes in the Arctic may contribute to increased turnover of organic carbon, resulting in higher CH 4 emissions. As the sole biological methane filter, methaneoxidizing bacteria (methanotrophs) are important controllers in this process. While both alpha-and gammaproteobacterial methanotrophs are present in circumpolar permafrost regions, including Canada, Siberia, and Svalbard, a dominance of the gammaproteobacterial genus Methylobacter was observed (8,10,14). Methylobacter tundripaludum SV96 was identified as an active methanotroph in its locus typicus by RNA-SIP (stable isotope probing) with 13 C methane (5, 15). The draft genome of M. tundripaludum SV96 was generated at the DOE Joint Genome Institute (JGI) using a combination of Illumina (1) and 454 technologies (9). The Illumina GAii shotgun library produced 41,446,074 reads (3,149.9 Mbp), a 454 Titanium standard library yielded 500,724 reads, and a paired-end 454 library (7-kb average insert size) delivered 271,299 reads. The 220.6 Mbp of 454 data were assembled with Newbler (version 2.3). Illumina data were assembled with VELVET, version 1.0.13 (16). Reads were assembled after computational shredding using parallel phrap (SPS version 4.24; High Performance Software, LLC). Consed software (2, 3, 4) was used for finishing. Potential base errors and consensus quality were corrected using Illumina data and Polisher software (A. Lapidus, unpublished data). Possible misassemblies were corrected using gapResolution (C. Han, unpublished data), Dupfinisher (6), or sequencing of subcloned bridging PCR fragments. Gaps between contigs were closed by PCR or bubble PCR primer walks using Consed (J.-F. Cheng, unpublished data). Gaps were closed with 1,095 PCRs, yielding a sequence of 3 contigs (2,936,421, 367,513, and 1,544,395 bp). The final assembly represents 190.8 Mbp of 454 data and 2,930.7 Mbp of Illumina data. Sequence annotation and comparative genome analysis are under way with assistance from the MicroScope platform at Genoscope (13).The M. tundripaludum SV96 genome contains one operon for particulate methane monooxygenase (pmoCAB) and the recently discovered pxm operon (pxmABC), encoding a copper membrane monooxy...

Sulfuricurvum kujiense Kodama and Watanabe 2004 is the type species of the monotypic genus Sulfuricurvum, which belongs to the family Helicobacteraceae in the class Epsilonproteobacteria. The species is of interest because it is frequently found in crude oil and oil sands where it utilizes various reduced sulfur compounds such as elemental sulfur, sulfide and thiosulfate as electron donors. Members of the species do not utilize sugars, organic acids or hydrocarbons as carbon and energy sources. This genome sequence represents the type strain of the only species in the genus Sulfuricurvum. The genome, which consists of a circular chromosome of 2,574,824 bp length and four plasmids of 118,585 bp, 71,513 bp, 51,014 bp, and 3,421 bp length, respectively, harboring a total of 2,879 protein-coding and 61 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Olsenella uli (Olsen et al. 1991) Dewhirst et al. 2001 is the type species of the genus Olsenella, which belongs to the actinobacterial family Coriobacteriaceae. The species is of interest because it is frequently isolated from dental plaque in periodontitis patients and can cause primary endodontic infection. The species is a Gram-positive, non-motile and non-sporulating bacterium. The strain described in this study was isolated from human gingival crevices. This is the first completed sequence of the genus Olsenella and the fifth sequence from a member of the family Coriobacteriaceae. The 2,051,896 bp long genome with its 1,795 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.