Targeting Homologous Recombination in Notch-Driven C. elegans Stem Cell and Human Tumors

Mammalian NOTCH1-4 receptors are all associated with human malignancy, although exact roles remain enigmatic. Here we employ glp-1(ar202), a temperature-sensitive gain-of-function C. elegans NOTCH mutant, to delineate NOTCH-driven tumor responses to radiotherapy. At ≤20°C, glp-1(ar202) is wild-type, whereas at 25°C it forms a germline stem cell⁄progenitor cell tumor reminiscent of human cancer. We identify a NOTCH tumor phenotype in which all tumor cells traffic rapidly to G2⁄M post-irradiation, attempt to repair DNA strand breaks exclusively via homology-driven repair, and when this fails die by mitotic death. Homology-driven repair inactivation is dramatically radiosensitizing. We show that these concepts translate directly to human cancer models.     

Microbial Communities Associated with Healthy and White Syndrome-Affected Echinopora lamellosa in Aquaria and Experimental Treatment with the Antibiotic Ampicillin

Prokaryotic and ciliate communities of healthy and aquarium White Syndrome (WS)-affected coral fragments were screened using denaturing gradient gel electrophoresis (DGGE). A significant difference (R = 0.907, p < 0.001) in 16S rRNA prokaryotic diversity was found between healthy (H), sloughed tissue (ST), WS-affected (WSU) and antibiotic treated (WST) samples. Although 3 Vibrio spp were found in WS-affected samples, two of these species were eliminated following ampicillin treatment, yet lesions continued to advance, suggesting they play a minor or secondary role in the pathogenesis. The third Vibrio sp increased slightly in relative abundance in diseased samples and was abundant in non-diseased samples. Interestingly, a Tenacibaculum sp showed the greatest increase in relative abundance between healthy and WS-affected samples, demonstrating consistently high abundance across all WS-affected and treated samples, suggesting Tenacibaculum sp could be a more likely candidate for pathogenesis in this instance. In contrast to previous studies bacterial abundance did not vary significantly (ANOVA, F2, 6 = 1.000, p = 0.422) between H, ST, WSU or WST. Antimicrobial activity (assessed on Vibrio harveyi cultures) was limited in both H and WSU samples (8.1% ±8.2 and 8.0% ±2.5, respectively) and did not differ significantly (Kruskal-Wallis, χ2 (2) = 3.842, p = 0.146). A Philaster sp, a Cohnilembus sp and a Pseudokeronopsis sp. were present in all WS-affected samples, but not in healthy samples. The exact role of ciliates in WS is yet to be determined, but it is proposed that they are at least responsible for the neat lesion boundary observed in the disease.     

An initial top-down proteomic analysis of the standard cuprizone mouse model of multiple sclerosis

An initial proteomic analysis of the cuprizone mouse model to characterise the breadth of toxicity by assessing cortex, skeletal muscle, spleen and peripheral blood mononuclear cells. Cuprizone treated vs. control mice for an initial characterisation. Select tissues from each group were pooled, analysed in triplicate using two-dimensional gel electrophoresis (2DE) and deep imaging and altered protein species identified using liquid chromatography tandem mass spectrometry (LC/MS/MS). Forty-three proteins were found to be uniquely detectable or undetectable in the cuprizone treatment group across the tissues analysed. Protein species identified in the cortex may potentially be linked to axonal damage in this model, and those in the spleen and peripheral blood mononuclear cells to the minimal peripheral immune cell infiltration into the central nervous system during cuprizone mediated demyelination. Primary oligodendrocytosis has been observed in type III lesions in multiple sclerosis. However, the underlying mechanisms are poorly understood. Cuprizone treatment results in oligodendrocyte apoptosis and secondary demyelination. This initial analysis identified proteins likely related to axonal damage; these may link primary oligodendrocytosis and secondary axonal damage. Furthermore, this appears to be the first study of the cuprizone model to also identify alterations in the proteomes of skeletal muscle, spleen and peripheral blood mononuclear cells. Notably, protein disulphide isomerase was not detected in the cuprizone cohort; its absence has been linked to reduced major histocompatibility class I assembly and reduced antigen presentation. Overall, the results suggest that, like experimental autoimmune encephalomyelitis, results from the standard cuprizone model should be carefully considered relative to clinical multiple sclerosis.     

Conserved water-mediated H-bonding dynamics of catalytic Asn 175 in plant thiol protease

The role of invariant water molecules in the activity of plant cysteine protease is ubiquitous in nature. On analysing the 11 different Protein DataBank (PDB) structures of plant thiol proteases, the two invariant water molecules W1 and W2 (W220 and W222 in the template 1PPN structure) were observed to form H-bonds with the O_b atom of Asn 175. Extensive energy minimization and molecular dynamics simulation studies up to 2 ns on all the PDB and solvated structures clearly revealed the involvement of the H-bonding association of the two water molecules in fixing the orientation of the asparagine residue of the catalytic triad. From this study, it is suggested that H-bonding of the water molecule at the W1 invariant site better stabilizes the Asn residue at the active site of the catalytic triad.     

A protocol for temporal calibration of general area cladograms

Aim To describe a protocol for incorporating a temporal dimension into historical biogeographical analysis, while maintaining the essential independence of all datasets, involving the generation of general area cladograms. Location Global. Methods General area cladograms (GACs) are a reconstruction of the evolutionary history of a set of areas and unrelated clades within those areas. Nodes on a GAC correspond to speciation events in a group of taxa; general nodes are those at which multiple unrelated clades speciate. We undertake temporal calibration of GACs using molecular clock estimates of splitting events between extant taxa as well as first appearance data from the fossil record. We present two examples based on re‐analysis of previously published data: first, a temporally calibrated GAC generated from secondary Brooks parsimony analysis (BPA) of six extant bird clades from the south‐west of North America using molecular clock estimates of divergence times; and second, an analysis of African Neogene mammals based on a phylogenetic analysis for comparing trees (PACT) analysis. Results A hypothetical example demonstrates how temporal calibration reveals potentially critical information about the timing of both unique and general events, while also illustrating instances of incongruence between dates generated from molecular clock estimates and fossils. For the African Neogene mammal dataset, our analysis reveals that most mammal clades underwent geodispersal associated with the Neogene climatic optimum (c. 16 Ma) and vicariant speciation in central Africa correlated with increased aridity and cooler temperatures around 2.5 Ma. Main conclusions Temporally calibrated GACs are valuable tools for assessing whether coordinated patterns of speciation are associated with large‐scale climatic or tectonic phenomena.     

Ontogeny and homology of the skeletal elements that form the sucking disc of remoras (Teleostei,Echeneoidei, Echeneidae)

The sucking disc of the sharksuckers of the family Echeneidae is one of the most remarkable and most highly modified skeletal structures among vertebrates. We studied the development of the sucking disc based on a series of larval, juvenile, and adult echeneids ranging from 9.3 mm to 175 mm standard length. We revisited the question of the homology of the different skeletal parts that form the disc using an ontogenetic approach. We compared the initial stages of development of the disc with early developmental stages of the spinous dorsal fin in a representative of the morphologically basal percomorph Morone. We demonstrate that the “interneural rays” of echeneids are homologous with the proximal‐middle radials of Morone and other teleosts and that the “intercalary bones” of sharksuckers are homologous with the distal radials of Morone and other teleosts. The “intercalary bones” or distal radials develop a pair of large wing‐like lateral extensions in echeneids, not present in this form in any other teleost. Finally the “pectinated lamellae” are homologous with the fin spines of Morone and other acanthomorphs. The main part of each pectinated lamella is formed by bilateral extensions of the base of the fin spine just above its proximal tip, each of which develops a row of spinous projections, or spinules, along its posterior margin. The number of rows and the number of spinules increase with size, and they become autogenous from the body of the lamellae. We also provide a historical review of previous studies on the homology of the echeneid sucking disc and demonstrate that the most recent hypotheses, published in 2002, 2005 and 2006, are erroneous. J. Morphol. 2012. © 2012 Wiley Periodicals, Inc.