Implementation of Organ Culture storage of donor corneas: a 3 year study of its impact on the corneal transplant wait list at the Lions New South Wales Eye Bank

Organ Culture corneal storage offers an extended storage time and increased donor pool and tissue assessment opportunities. In September 2011, the Lions New South Wales Eye Bank (LNSWEB) moved from hypothermic storage to Organ Culture corneal storage. This study evaluates the impact of implementation of Organ Culture on donor eye retrieval and the corneal transplant waiting list over a 3 year period in NSW, Australia. Retrospective review of the LNSWEB data from September 2011 to August 2014. Tissue collection, waiting list and tissue utilization data were recorded. The data from September 2008 to August 2011 for Optisol-GS storage was used for comparison. The annual donor and cornea collection rate increased 35 % and 44 % respectively with Organ Culture compared to Optisol-GS storage. The utilization rate of corneal tissue increased from 73.4 % with hypothermic storage to 77.2 % with Organ Culture storage. The transplant wait list decreased by 77.3 % from September 2011 to August 2014 and correlated with the increased rate of corneal transplantation (r = ?0.9381, p < 0.0001). No other factors impacting the wait list changed over this period. Corneas not used from either storage method were due to unacceptable endothelial cell density/viability. The contamination rate of corneas stored in Organ Culture medium was low at 1.74 %. The Organ Culture storage method increases the corneal donor pool available to Eye banks. The practical benefits of the extended storage time and increased donor assessment opportunities have directly led to an increase in corneal utilization rate and a significant decrease in recipient wait list time.     

Laboratory evaluation of crude oil biodegradation with commercial or natural microbial inocula.

Experiments have been performed to screen eight microbial commercial products that, according to the manufacturers, are able to degrade crude oil. This study compared the crude oil biodegradation activity of commercial inocula with that of natural inocula (activated sludge and tropical aquarium water). Some of the latter were previously adapted to the crude oil as the only carbon source. Nutrients and sorbents in the commercial formulations were eliminated, and each inoculum was precultured on marine yeast extract medium. Crude oil biodegradability tests were conducted with close initial substrate concentration to initial bacterial concentration ratios (S0/X0) of 0.94 g of crude oil/10(9) CFU, which allowed a comparison of biodegradation activity. The inocula oxidized the crude oil after a short lag time of less than 3-18 days. After that time, the rate of oxidation varied between 45 and 244 mg O2/(L.day). Crude oil biodegradation after a 28-day test was effective only for 10 out of 12 inocula (from 0.1 to 25% in weight). Biodegradation mainly corresponded to the saturated fraction of the crude oil; the asphaltene fraction was never significantly biodegraded. Our results led to the conclusion that natural inocula, either adapted or not adapted to crude oil, were the most active (from 16 to 25% of loss in crude oil weight) and only one commercial inoculum was able to degrade 18% of the crude oil. Other inocula had a biodegradation activity ranging from 0.1 to 14%.     

The structure of a cypovirus and the functional organization of dsRNA viruses.

Cytoplasmic polyhedrosis virus (CPV) is unique among the double-stranded RNA viruses of the family Reoviridae in having a single capsid layer. Analysis by cryo-electron microscopy allows comparison of the single shelled CPV and orthoreovirus with the high resolution crystal structure of the inner shell of the bluetongue virus (BTV) core. This suggests that the novel arrangement identified in BTV, of 120 protein subunits in a so-called 'T=2' organization, is a characteristic of the Reoviridae and allows us to delineate structural similarities and differences between two subgroups of the family--the turreted and the smooth-core viruses. This in turn suggests a coherent picture of the structural organization of many dsRNA viruses.     

Mutations Affecting the Ability of the Escherichia coli UmuD′ Protein To Participate in SOS Mutagenesis

The products of the SOS-regulated umuDC operon are required for most UV and chemical mutagenesis in Escherichia coli, a process that results from a translesion synthesis mechanism. The UmuD protein is activated for its role in mutagenesis by a RecA-facilitated autodigestion that removes the N-terminal 24 amino acids. A previous genetic screen for nonmutable umuD mutants had resulted in the isolation of a set of missense mutants that produced UmuD proteins that were deficient in RecA-mediated cleavage (J. R. Battista, T. Ohta, T. Nohmi, W. Sun, and G. C. Walker, Proc. Natl. Acad. Sci. USA 87:7190–7194, 1990). To identify elements of the UmuD′ protein necessary for its role in translesion synthesis, we began with umuD′, a modified form of the umuD gene that directly encodes the UmuD′ protein, and obtained missense umuD′ mutants deficient in UV and methyl methanesulfonate mutagenesis. The D39G, L40R, and T51I mutations affect residues located at the UmuD′₂ homodimer interface and interfere with homodimer formation in vivo. The D75A mutation affects a highly conserved residue located at one end of the central strand in a three-stranded β-sheet and appears to interfere with UmuD′₂ homodimer formation indirectly by affecting the structure of the UmuD′ monomer. When expressed from a multicopy plasmid, the L40R umuD′ mutant gene exhibited a dominant negative effect on a chromosomal umuD⁺ gene with respect to UV mutagenesis, suggesting that the mutation has an effect on UmuD′ function that goes beyond its impairment of homodimer formation. The G129D mutation affects a highly conserved residue that lies at the end of the long C-terminal β-strand and results in a mutant UmuD′ protein that exhibits a strongly dominant negative effect on UV mutagenesis in a umuD⁺ strain. The A30V and E35K mutations alter residues in the N-terminal arms of the UmuD′₂ homodimer, which are mobile in solution.     

Vegetation quality and habitat selection by European haresLepus europaeus in a pastural landscape

European haresLepus europaeus Pallas, 1778 have lower population densities and body condition in pastural landscapes than in arable landscapes, but reasons for this are not understood. The aim of this study was to determine whether forage quality is low in pastural landscapes during certain seasons. We carried out chemical analysis of the nutritional quality of 5 habitat types to determine whether hares select high quality habitats, and whether nutritional quality explains seasonal differences in range sizes of hares in pastural landscapes. Hares did not tend to select habitats of high nutritional quality (protein, fat or energy) over those of lower quality. Hares did not increase active range size as the overall energy content of forage at the study site decreased; seasonal differences in active range size were not explained by nutritional quality. Differences may be explained by behavioural changes related to breeding. Pastural habitat is fairly stable in terms of nutritional quality through the year, and results suggest that poor forage quality is unlikely to be responsible for the poor body condition of hares in pastural landscapes. Hares in these landscapes are more likely to be limited by habitat quality in terms of cover than by forage.     

Dimorphic effects of Notch signaling in bone homeostasis

Notch signaling is a key mechanism in the control of embryogenesis. However, its in vivo function during mesenchymal cell differentiation, and, specifically, in bone homeostasis, remains largely unknown. Here, we show that osteoblast-specific gain of Notch function causes severe osteosclerosis owing to increased proliferation of immature osteoblasts. Under these pathological conditions, Notch stimulates early osteoblastic proliferation by upregulating the genes encoding cyclin D, cyclin E and Sp7 (osterix). The intracellular domain of Notch1 also regulates terminal osteoblastic differentiation by directly binding Runx2 and repressing its transactivation function. In contrast, loss of all Notch signaling in osteoblasts, generated by deletion of the genes encoding presenilin-1 and presenilin-2 in bone, is associated with late-onset, age-related osteoporosis, which in turn results from increased osteoblast-dependent osteoclastic activity due to decreased osteoprotegerin mRNA expression in these cells. Together, these findings highlight the potential dimorphic effects of Notch signaling in bone homeostasis and may provide direction for novel therapeutic applications.     

Insights into virus evolution and membrane biogenesis from the structure of the marine lipid-containing bacteriophage PM2

Recent, primarily structural observations indicate that related viruses, harboring no sequence similarity, infect hosts of different domains of life. One such clade of viruses, defined by common capsid architecture and coat protein fold, is the so-called PRD1-adenovirus lineage. Here we report the structure of the marine lipid-containing bacteriophage PM2 determined by crystallographic analyses of the entire approximately 45 MDa virion and of the outer coat proteins P1 and P2, revealing PM2 to be a primeval member of the PRD1-adenovirus lineage with an icosahedral shell and canonical double beta barrel major coat protein. The view of the lipid bilayer, richly decorated with membrane proteins, constitutes a rare visualization of an in vivo membrane. The viral membrane proteins P3 and P6 are organized into a lattice, suggesting a possible assembly pathway to produce the mature virus.     

Assembly reconciliation

MOTIVATION: Many genomes are sequenced by a collaboration of several centers, and then each center produces an assembly using their own assembly software. The collaborators then pick the draft assembly that they judge to be the best and the information contained in the other assemblies is usually not used. METHODS: We have developed a technique that we call assembly reconciliation that can merge draft genome assemblies. It takes one draft assembly, detects apparent errors, and, when possible, patches the problem areas using pieces from alternative draft assemblies. It also closes gaps in places where one of the alternative assemblies has spanned the gap correctly. RESULTS: Using the Assembly Reconciliation technique, we produced reconciled assemblies of six Drosophila species in collaboration with Agencourt Bioscience and The J. Craig Venter Institute. These assemblies are now the official (CAF1) assemblies used for analysis. We also produced a reconciled assembly of Rhesus Macaque genome, and this assembly is available from our website http://www.genome.umd.edu. AVAILABILITY: The reconciliation software is available for download from http://www.genome.umd.edu/software.htm