The extracellular matrix microtopography drives critical changes in cellular motility and Rho A activity in colon cancer cells

We have shown that the microtopography (mT) underlying colon cancer changes as a tumor de-differentiates. We distinguish the well-differentiated mT based on the increasing number of "pits" and poorly differentiated mT on the basis of increasing number of "posts." We investigated Rho A as a mechanosensing protein using mT features derived from those observed in the ECM of colon cancer. We evaluated Rho A activity in less-tumorogenic (Caco-2 E) and more tumorigenic (SW620) colon cancer cell-lines on microfabricated pits and posts at 2.5 μm diameter and 200 nm depth/height. In Caco-2 E cells, we observed a decrease in Rho A activity as well as in the ratio of G/F actin on surfaces with either pits or posts but despite this low activity, knockdown of Rho A led to a significant decrease in confined motility suggesting that while Rho A activity is reduced on these surfaces it still plays an important role in controlling cellular response to barriers. In SW620 cells, we observed that Rho A activity was greatest in cells plated on a post microtopography which led to increased cell motility, and an increase in actin cytoskeletal turnover.     

The Impact of Prolonged Storage of Red Blood Cells on Cancer Survival

Background

The duration of storage of transfused red blood cells (RBC) has been associated with poor clinical outcomes in some studies. We sought to establish whether prolonged storage of transfused RBC in cancer patients influences overall survival (OS) or cancer recurrence.

Methods and Findings

Patients diagnosed with cancer at The Ottawa Regional Cancer Centre between January 01, 2000 and December 31, 2005 were included (n = 27,591) where 1,929 (7.0%) received RBC transfusions within one year from diagnosis. Transfused RBC units were categorized as “new” if stored for less than 14 days, “intermediate” if stored between 14 and 28 days and “old” if stored for more than 28 days. Baseline characteristics between the comparative groups were compared by ANOVA test. Categorical variables and continuous variables were compared using Chi-squared and Wilcoxan rank-sum tests respectively. Overall survival was not associated with duration of storage of transfused RBC with a median survival of 1.2, 1.7, 1.1 years for only new, intermediate and old RBC units respectively (p = 0.36). Cancer recurrence was significantly higher in patients who received a RBC transfusion than those who did not (56.3% vs 33.0% respectively; p<0.0001) but was not affected by the duration of storage of transfused RBC (p = 0.06). In multivariate analysis, lung cancer, advanced stage, chemotherapy, radiation, cancer-related surgery and cancer recurrence were associated with inferior OS (p<0.05), while age, advanced stage, lung cancer, and more than 6 units of blood transfused were associated with cancer recurrence (p<0.05). The duration of storage of RBC before transfusion was not associated with OS or cancer recurrence in multivariate analysis.

Conclusion

In patients diagnosed with cancer, the duration of storage of transfused RBC had no impact on OS or cancer recurrence. This suggests that our current RBC storage policy of providing RBC of variable duration of storage for patients with malignancy is safe.     

Neural development in human embryonic stem cells-applications of lentiviral vectors

The derivation of neural lineages from human embryonic stem cells (hESCs) in vitro is based largely on exposure of hESCs to exogenous signals and substrates, designed to mimic conditions in the developing embryo. However, selection of specific lineages and the discovery of gene function in human neural development may be enhanced by the ability to intrinsically regulate gene expression. Recombinant lentiviral vectors provide an efficient method to stably introduce genes into hESC and their differentiating derivatives. Here we review the methods used to derive neural cells from hESCs, transduction of these cells with lentiviral vectors, and improvements that have been made to the vectors to enhance viral integration and transgene expression. Finally, we explore prospects for future uses of lentiviral vectors in hESC research, including their applications in library screening for drug development, zinc finger nucleases for gene editing and optogenetics to interrogate cellular pathways and function.     

A unified theory for upscaling aerobic granular sludge sequencing batch reactors

Aerobic granular sludge sequencing batch reactors (SBR) are a promising technology for treating wastewater. Increasing evidence suggests that aerobic granulation in SBRs is driven by selection pressures exerted on microorganisms. Three major selection pressures have been identified as follows: settling time, volume exchange ratio and discharge time. This review demonstrates that these three major selection pressures can all be unified to one, the minimal settling velocity of bio-particles, that determines aerobic granulation in SBRs. The unified selection pressure theory is a useful guide for manipulating and optimizing the formation and characteristics of aerobic granules in SBRs. Furthermore, the unified theory provides a single engineering basis for scale up of aerobic granular sludge SBRs.     

Divide-and-conquer approach for the exemplar breakpoint distance

MOTIVATION: A one-to-one correspondence between the sets of genes in the two genomes being compared is necessary for the notions of breakpoint and reversal distances. To compare genomes where there are paralogous genes, Sankoff formulated the exemplar distance problem as a general version of the genome rearrangement problem. Unfortunately, the problem is NP-hard even for the breakpoint distance. RESULTS: This paper proposes a divide-and-conquer approach for calculating the exemplar breakpoint distance between two genomes with multiple gene families. The combination of our approach and Sankoff's branch-and-bound technique leads to a practical program to answer this question. Tests with both simulated and real datasets show that our program is much more efficient than the existing program that is based only on the branch-and-bound technique. AVAILABILITY: Code for the program is available from the authors.     

Microbial adaptation to biodegradation of tert-butyl alcohol in a sequencing batch reactor

This study demonstrates the utility of the sequencing batch reactor (SBR) to adapt microorganisms towards biological removal of tert-butyl alcohol (TBA). The reactor was inoculated with activated sludge and fed with TBA as the sole carbon source. Start-of-cycle TBA concentrations were initially set at 100 mgL(-1) with a cycle time of 24 h and a volumetric exchange ratio of 50% to maintain a TBA loading rate of not more than 100 mgL(-1)d(-1). Step increases in TBA loading rates up to 600 mgL(-1)d(-1) were achieved by first raising the start-of-cycle TBA concentration to 150 mgL(-1) on day 90 and subsequently by reducing the cycle time from 24 to 12, 8 and 6h on days 100, 121 and 199, respectively. This acclimation strategy favored the retention of increasingly higher densities of well-adapted microbial populations in the reactor. The increases in TBA loading produced better settling biomass and higher biomass concentrations with higher specific TBA biodegradation rates. Effluent TBA concentrations were consistently below the detection limit of 25 microgL(-1). The use of progressively shorter cycle times created selection pressures that fostered the self-immobilization of the reactor microorganisms into aerobic granules which first appeared on day 125. Specific TBA biodegradation rates in the granules followed the Haldane model for substrate inhibition, and peaked at 13.8 mgTBAgVSS(-1)h(-1) at a TBA concentration of 300 mgL(-1). Denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA genes from granules sampled between days 220 and 247 confirmed the existence of a highly stable microbial community with members belonging to the alpha, beta and delta subdivisions of Proteobacteria and the Cytophaga-Flavobacteria-Bacteroides (CFB) group.     

The mycological and molecular study of <Emphasis Type="Italic">Hortaea werneckii</Emphasis> isolated from blood and splenic abscess

Hortaea werneckii is an environmental dematiaceous fungus found in the halophilic environment. It causes tinea nigra. We report the isolation of H. werneckii from blood and splenic abscess of two patients with acute myelomonocytic leukaemia. H. werneckii grew at room temperature but not at 37 °C, it was identified by biochemical tests, growth characteristics and the presence of conspicuous collarette intercalary on dividing yeast cells. The use of specific oligonucleotide primer Hor-F (5′-TGGACACCTTCA TAACTCTTG-3′) and Hor-R (5′-TCACAACGCTTAGAGACGG-3′) confirmed the two isolates were H. werneckii. The sequence for 281 nucleotide of HW299 and HW403 were 99% identical but differed only in one nucleotide. In vitro anti-fungal susceptibility testing showed that the isolates were resistant to amphotericin B and flucytosine.     

Induction of cytokine expression in rat post-ischemic sinoatrial node (SAN)

The aim of this study was to determine the spatial and temporal expression of various pro-inflammatory cytokines in the peri-sinoatrial nodal area after atrial infarction. Rats were subjected to permanent atrial infarction, in particular, sinoatrial node (SAN) infarction and sacrificed at various time points up to 7 days. Real-time polymerase chain reaction analysis demonstrated that mRNA levels of tumor necrosis factor alpha (TNF-alpha), interleukin-1beta, interleukin-6, and transforming growth factor beta 1 (TGF-beta(1)) were upregulated in the peri-sinoatrial nodal area after atrial infarction. Immunostaining for TNF-alpha and TGF-beta(1) proteins revealed that both cytokines were expressed persistently up to 7 days after atrial infarction around the peri-sinoatrial nodal area. Furthermore, the infiltrating inflammatory cells immunoreactive for both cytokines were predominant within the infarct SAN. In situ hybridization analysis showed that TNF-alpha gene expression was enhanced in the inflammatory cells and myocardium within the peri-sinoatrial nodal area in response to the infarction. These results provide evidence for the local expression of cytokines in the post-ischemic peri-sinoatrial nodal area, suggesting that the upregulation of the cytokines might be associated with the atrial arrhythmia observed after acute myocardial infarction.     

Bacillus naphthovorans sp. nov. from oil-contaminated tropical marine sediments and its role in naphthalene biodegradation

A Bacillus sp., designated as strain MN-003, was isolated as the dominant cultivatable naphthalene-degrading organism from oil-contaminated tropical marine sediments. Strain MN-003 is strictly aerobic, rod-shaped, Gram-positive, catalase positive, oxidase negative, and forms endospores. Strain MN-003 grew at salinities ranging from 0.28 to 7.00% and temperatures ranging from 15 to 41 degrees C. Phylogenetic analyses reveal that strain MN-003 is most similar to Bacillus sp. VAN14, with a 16S rRNA sequence identity of 97.9%. Based on taxonomic and 16S rRNA data, strain MN-003 was named Bacillus naphthovorans sp. nov. When grown with naphthalene as sole carbon source, strain MN-003 had a maximal specific growth rate (mu(max)) of 0.32 +/- 0.03 h(-1), and a half-saturation constant (K(S)) of 22.3 +/-4.2 microM. A batch study of the tropical marine sediments enriched with naphthalene showed that cells of the Bacillus genus grew to become dominant members of the microbial community. The bacilli comprised 39.5 +/- 6.5% of the microbial fraction after 20 days of enrichment.