Biomimetic micropatterned multi-channel nerve guides by templated electrospinning

This report describes a new approach for fabricating microchannels within three-dimensional electrospun constructs. These key features serve to mimic the fascicular architecture and fibrous extracellular matrix found in native nerve. Both electrospun fibers and multi-channeled structure nerve guides have become areas of increasing interest for their beneficial roles in nerve repair. However, to the best of our knowledge, this is the first report of a guide that incorporates both. Multiple parallel channels provide a greater number of defined paths and increased surface area compared to cylindrical guides. Additionally, the fibrous nature of electrospun fibers permits better mass transport than solid-walled constructs. The flexible fabrication scheme allows tailoring of nerve guide parameters such as channel diameters ranging from 33 to 176 μm and various wall thicknesses. Channel and fiber structures were assessed by optical and electron microscope images. Geometric calculations estimated a porosity of over 85% for these guides with 16% or less from the channels. In vitro culture with Schwann cells demonstrated cellular infiltration into channels with restricted migration between fibers. Finally, cell proliferation and survival throughout the guide indicates that this design warrants future in vivo examination.     

Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T))

Thermodesulfatator indicus Moussard et al. 2004 is a member of the Thermodesulfobacteriaceae, a family in the phylum Thermodesulfobacteria that is currently poorly characterized at the genome level. Members of this phylum are of interest because they represent a distinct, deep-branching, Gram-negative lineage. T. indicus is an anaerobic, thermophilic, chemolithoautotrophic sulfate reducer isolated from a deep-sea hydrothermal vent. Here we describe the features of this organism, together with the complete genome sequence, and annotation. The 2,322,224 bp long chromosome with its 2,233 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6)

Hydrogenobacter thermophilus Kawasumi et al. 1984 is the type species of the genus Hydrogenobacter. H. thermophilus was the first obligate autotrophic organism reported among aerobic hydrogen-oxidizing bacteria. Strain TK-6(T) is of interest because of the unusually efficient hydrogen-oxidizing ability of this strain, which results in a faster generation time compared to other autotrophs. It is also able to grow anaerobically using nitrate as an electron acceptor when molecular hydrogen is used as the energy source, and able to aerobically fix CO(2)via the reductive tricarboxylic acid cycle. This is the fifth completed genome sequence in the family Aquificaceae, and the second genome sequence determined from a strain derived from the original isolate. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,742,932 bp long genome with its 1,899 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Complete genome sequence of Oceanithermus profundus type strain (506)

Oceanithermus profundus Miroshnichenko et al. 2003 is the type species of the genus Oceanithermus, which belongs to the family Thermaceae. The genus currently comprises two species whose members are thermophilic and are able to reduce sulfur compounds and nitrite. The organism is adapted to the salinity of sea water, is able to utilize a broad range of carbohydrates, some proteinaceous substrates, organic acids and alcohols. This is the first completed genome sequence of a member of the genus Oceanithermus and the fourth sequence from the family Thermaceae. The 2,439,291 bp long genome with its 2,391 protein-coding and 54 RNA genes consists of one chromosome and a 135,351 bp long plasmid, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Complete genome sequence of Bacteroides helcogenes type strain (P 36-108)

Bacteroides helcogenes Benno et al. 1983 is of interest because of its isolated phylogenetic location and, although it has been found in pig feces and is known to be pathogenic for pigs, occurrence of this bacterium is rare and it does not cause significant damage in intensive animal husbandry. The genome of B. helcogenes P 36-108(T) is already the fifth completed and published type strain genome from the genus Bacteroides in the family Bacteroidaceae. The 3,998,906 bp long genome with its 3,353 protein-coding and 83 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Shifting the balance from qualitative to quantitative analysis of arbuscular mycorrhizal communities in field soils

Population studies of arbuscular mycorrhizal fungi (AMF) have traditionally been achieved by indirect analyses of soil-borne spore populations. These studies are not necessarily reflective of populations of AMF within the roots. Advances in molecular biology have revolutionized the analysis of fungal populations colonizing roots and forming mycorrhizas. Initially these studies were qualitative and reported presence or absence of particular AMF species in soils or in roots for comparison between different environments. More recently, the methodology has developed for direct quantification of AMF within roots. Quantitative PCR provides the means to study spatial distribution and individual quantification of AMF in mixed communities over time. In this review, we discuss the progress and application of indirect, direct and finally quantitative methodologies for studying arbuscular mycorrhizal communities. We conclude that the molecular tools now exist to quantitatively analyse the effect of environment, management or inoculation of soils on AMF communities within roots.     

Effects of moderate ammonium enrichment on three submersed macrophytes under contrasting light availability

1. Increased ammonium concentrations and decreased light availability in a water column have been reported to adversely affect submersed vegetation in eutrophic waters worldwide. 2. We studied the chronic effects of moderate enrichment (NH₄–N: 0.16–0.25 mg L^?1) on the growth and carbon and nitrogen metabolism of three macrophytes (Ceratophyllum demersum, Myriophyllum spicatum and Vallisneria natans) under contrasting light availability in a 2‐month experiment. 3. The enrichment greatly increased the contents of free amino acids and nitrogen in the shoot / leaf of the macrophytes. This indicates that was the dominant N source for the macrophytes. 4. Soluble carbohydrate contents remained relatively stable in the shoot / leaf of the macrophytes irrespective of the treatments. Under ambient light, the starch contents in the shoot / leaf of C. demersum and M. spicatum increased with enrichment, whereas V. natans did not exhibit any change. The starch contents decreased in C. demersum, increased in M. spicatum and remained unchanged in V. natans after the combined treatment of enrichment and reduced light. 5. The enrichment did not affect the growth of the three macrophytes under the ambient light. However, it did suppress the growth of C. demersum and M. spicatum under the reduced light. The results indicate that a moderate enrichment was not directly toxic to the macrophytes although it might change their viability in eutrophic lakes in terms of the carbon and nitrogen metabolism.     

Bacteria engineered for fuel ethanol production: current status

The lack of industrially suitable microorganisms for converting biomass into fuel ethanol has traditionally been cited as a major technical roadblock to developing a bioethanol industry. In the last two decades, numerous microorganisms have been engineered to selectively produce ethanol. Lignocellulosic biomass contains complex carbohydrates that necessitate utilizing microorganisms capable of fermenting sugars not fermentable by brewers' yeast. The most significant of these is xylose. The greatest successes have been in the engineering of Gram-negative bacteria: Escherichia coli, Klebsiella oxytoca, and Zymomonas mobilis. E. coli and K. oxytoca are naturally able to use a wide spectrum of sugars, and work has concentrated on engineering these strains to selectively produce ethanol. Z. mobilis produces ethanol at high yields, but ferments only glucose and fructose. Work on this organism has concentrated on introducing pathways for the fermentation of arabinose and xylose. The history of constructing these strains and current progress in refining them are detailed in this review.