Genomic Analysis of Sleeping Beauty Transposon Integration in Human Somatic Cells

The Sleeping Beauty (SB) transposon is a non-viral integrating vector system with proven efficacy for gene transfer and functional genomics. However, integration efficiency is negatively affected by the length of the transposon. To optimize the SB transposon machinery, the inverted repeats and the transposase gene underwent several modifications, resulting in the generation of the hyperactive SB100X transposase and of the high-capacity “sandwich” (SA) transposon. In this study, we report a side-by-side comparison of the SA and the widely used T2 arrangement of transposon vectors carrying increasing DNA cargoes, up to 18 kb. Clonal analysis of SA integrants in human epithelial cells and in immortalized keratinocytes demonstrates stability and integrity of the transposon independently from the cargo size and copy number-dependent expression of the cargo cassette. A genome-wide analysis of unambiguously mapped SA integrations in keratinocytes showed an almost random distribution, with an overrepresentation in repetitive elements (satellite, LINE and small RNAs) compared to a library representing insertions of the first-generation transposon vector and to gammaretroviral and lentiviral libraries. The SA transposon/SB100X integrating system therefore shows important features as a system for delivering large gene constructs for gene therapy applications.     

Axitinib Improves Radiotherapy in Murine Xenograft Lung Tumors

A third of patients with non-small cell lung cancer (NSCLC) present with un-resectable stage III locally advanced disease and are currently treated by chemo-radiotherapy but the median survival is only about 21 months. Using an orthotopic xenograft model of lung carcinoma, we have investigated the combination of radiotherapy with the anti-angiogenic drug axitinib (AG-013736, Pfizer), which is a small molecule receptor tyrosine kinase inhibitor that selectively targets the signal transduction induced by VEGF binding to VEGFR receptors. We have tested the combination of axitinib with radiotherapy in nude mice bearing human NSCLC A549 lung tumors. The therapy effect was quantitatively evaluated in lung tumor nodules. The modulation of radiation-induced pneumonitis, vascular damage and fibrosis by axitinib was assessed in lung tissue. Lung irradiation combined with long-term axitinib treatment was safe resulting in minimal weight loss and no vascular injury in heart, liver and kidney tissues. A significant decrease in the size of lung tumor nodules was observed with either axitinib or radiation, associated with a decrease in Ki-67 staining and a heavy infiltration of inflammatory cells in tumor nodules. The lungs of mice treated with radiation and axitinib showed a complete response with no detectable residual tumor nodules. A decrease in pneumonitis, vascular damage and fibrosis were observed in lung tissues from mice treated with radiation and axitinib. Our studies suggest that axitinib is a potent and safe drug to use in conjunction with radiotherapy for lung cancer that could also act as a radioprotector for lung tissue by reducing pneumonitis and fibrosis.     

Cephalopods in neuroscience: regulations,research and the 3Rs

Cephalopods have been utilised in neuroscience research for more than 100 years particularly because of their phenotypic plasticity, complex and centralised nervous system, tractability for studies of learning and cellular mechanisms of memory (e.g. long-term potentiation) and anatomical features facilitating physiological studies (e.g. squid giant axon and synapse). On 1 January 2013, research using any of the about 700 extant species of “live cephalopods” became regulated within the European Union by Directive 2010/63/EU on the “Protection of Animals used for Scientific Purposes”, giving cephalopods the same EU legal protection as previously afforded only to vertebrates. The Directive has a number of implications, particularly for neuroscience research. These include: (1) projects will need justification, authorisation from local competent authorities, and be subject to review including a harm-benefit assessment and adherence to the 3Rs principles (Replacement, Refinement and Reduction). (2) To support project evaluation and compliance with the new EU law, guidelines specific to cephalopods will need to be developed, covering capture, transport, handling, housing, care, maintenance, health monitoring, humane anaesthesia, analgesia and euthanasia. (3) Objective criteria need to be developed to identify signs of pain, suffering, distress and lasting harm particularly in the context of their induction by an experimental procedure. Despite diversity of views existing on some of these topics, this paper reviews the above topics and describes the approaches being taken by the cephalopod research community (represented by the authorship) to produce “guidelines” and the potential contribution of neuroscience research to cephalopod welfare.     

Atg11 directs autophagosome cargoes to the PAS along actin cables

For more than 40 years, autophagy has been almost exclusively studied as a cellular response that allows adaptation to starvation situations. In nutrient-deprived conditions, cytoplasmic components and organelles are randomly sequestered into double-membrane vesicles called autophagosomes, creating the notion that this pathway is a nonselective process (reviewed in Refs 1, 2). Recent results, however, have demonstrated that under certain circumstances, cargoes such as protein complexes, organelles and bacteria can be selectively and exclusively incorporated into double-membrane vesicles.(1) We have recently shown that actin plays an essential role in two selective types of autophagy in the yeast Saccharomyces cerevisiae, the cytoplasm to vacuole targeting (Cvt) pathway and pexophagy, raising the possibility that the structures formed by polymers of this protein helps autophagosomes in recognizing the cargoes that must be delivered to the vacuole.(3) In this addendum, we discuss the possible central role of Atg11 as a molecule connecting cargoes, actin and pre-utophagosomal structure (PAS) elements.     

Spatial network structure and robustness of detritus-based communities in a patchy environment

The mechanisms that regulate the spatial distribution of species are an essential aid to understanding the effects of the environment on the persistence of populations and communities. The effects of spatial structure on the persistence and robustness of ecological communities can, in turn, prove useful in uncovering their functioning, e.g., in the decomposition of leaf detritus. We applied the framework of complex networks to evaluate the effects of spatial structure on the colonization process of leaf detritus in a patchy aquatic environment, with a spatial network of six pools at different salinity. We found three well-defined modules formed by groups of taxa sharing the same pools, observing an association between modularity and spatial proximity of pools. Modules maximize the number of links within modules, and minimize the number of links among modules, showing the presence of a strong site-specific association between taxa and pools. The topological characteristics of the network show robustness against random perturbations and a lower tolerance of targeted perturbations. These findings suggest that random events, such as flooding or heavy rains, slightly affect the robustness of the system, while localized perturbations on the most connected nodes could have a negative effect on the connectivity of the whole network. The consequences could lead to a structural and functional homogenization of the system, with potential effects for the entire trophic chain. Here we discuss the topological properties of the network in relation to the spatial distribution of pools, showing how network analysis can yield valuable insight for conservation and management.     

Subunit interfaces of oligomeric hyperthermophilic enzymes display enhanced compactness

Enzymes from thermophilic and, particularly, from hyperthermophilic organisms are surprisingly stable. Understanding the molecular origin of protein thermostability and thermoactivity attracted the interest of many scientists both for the perspective comprehension of the principles of protein structure and for the possible biotechnological applications through protein engineering. Comparative studies at sequence and structure levels were aimed at detecting significant differences of structural parameters related to protein stability between thermophilic and hyperthermophilic proteins and their mesophilic homologs. In a recent work, we focused attention on structural adaptation occurring at the subunit interface of oligomeric hyper- and thermostable enzymes. A set of structural and chemico-physical parameters were compared to those observed at the corresponding interfaces of homologous mesophilic proteins. Among the most significant variations, a general increase of interface apolarity and packing density in hyperthermophilic enzymes were found. This work was therefore aimed at elucidating whether the increased packing observed is reached also through the reduction of interface cavity number and volume. The results indicate that number of cavities tends to be relatively constant while cavity volume tends to decrease in the hyperthermophilic interfaces. The cavity apolarity increases in thermophiles but, apparently, not in hyperthermophiles. Moreover, interface hot spot residues of the mesophilic interfaces tend to be conserved in the extremophilic counterparts.     

Mosquito-Bacteria Symbiosis: The Case of Anopheles gambiae and Asaia

The symbiotic relationship between Asaia, an α-proteobacterium belonging to the family Acetobacteriaceae, and mosquitoes has been studied mainly in the Asian malaria vector Anopheles stephensi. Thus, we have investigated the nature of the association between Asaia and the major Afro-tropical malaria vector Anopheles gambiae. We have isolated Asaia from different wild and laboratory reared colonies of A. gambiae, and it was detected by PCR in all the developmental stages of the mosquito and in all the specimens analyzed. Additionally, we have shown that it localizes in the midgut, salivary glands and reproductive organs. Using recombinant strains of Asaia expressing fluorescent proteins, we have demonstrated the ability of the bacterium to colonize A. gambiae mosquitoes with a pattern similar to that described for A. stephensi. Finally, fluorescent in situ hybridization on the reproductive tract of females of A. gambiae showed a concentration of Asaia at the very periphery of the eggs, suggesting that transmission of Asaia from mother to offspring is likely mediated by a mechanism of egg-smearing. We suggest that Asaia has potential for use in the paratransgenic control of malaria transmitted by A. gambiae.     

On the catalytic role of the active site residue E121 of E. colil-aspartate oxidase

l-aspartate oxidase (LASPO) is a flavoenzyme catalyzing the first step in the de novo biosynthesis of NAD⁺. The enzyme oxidizes l-aspartate both under aerobic and anaerobic conditions using oxygen as well as fumarate as electron acceptor.     

The A1555G Mutation in the 12S rRNA Gene of Human mtDNA: Recurrent Origins and Founder Events in Families Affected by Sensorineural Deafness

The mtDNA variation of 50 Spanish and 4 Cuban families affected by nonsyndromic sensorineural deafness due to the A1555G mutation in the 12S rRNA gene was studied by high-resolution RFLP analysis and sequencing of the control region. Phylogenetic analyses of haplotypes and detailed survey of population controls revealed that the A1555G mutation can be attributed to >/=30 independent mutational events among the 50 Spanish families and that it occurs on mtDNA haplogroups that are common in all European populations. This indicates that the relatively high detection rate of this mutation in Spain is not due to sampling biases or to a single major founder event. Moreover, the distribution of these mutational events on different haplogroups is compatible with a random occurrence of the A1555G mutation and tends to support the conclusion that mtDNA backgrounds do not play a significant role in the expression of the mutation. Overall, these findings appear to indicate that the rare detection of this mutation in other populations is most likely due to inadequacy in patient ascertainment and molecular screening. This probable lack of identification of the A1555G mutation in subjects affected by sensorineural hearing loss implies that their maternally related relatives are not benefiting from presymptomatic detection and information concerning their increased risk of ototoxicity due to aminoglycoside treatments.