AtLACS7 interacts with the TPR domains of the PTS1 receptor PEX5

Long-chain acyl-CoA synthetases (LACSs) activate fatty acids for further metabolism and are encoded by a multi-gene family in Arabidopsis. AtLACS6 possesses a type 2 (PTS2) peroxisomal targeting sequence, whilst AtLACS7 has both a type 1 and type 2 peroxisomal targeting sequence. AtLACS7 was used as bait in a yeast two-hybrid screen. Multiple clones of the PTS1 receptor PEX5 were isolated. Quantitative beta-galactosidase assay indicated that full-length PEX5 interacts with AtLACS7 with higher affinity than the TPR domains alone. The interaction between PEX5 and AtLACS7 was confirmed by co-immunoprecipitation and shown to be specific for the PTS1, therefore the AtLACS7 PTS1 is accessible to bind PEX5 in the full-length AtLACS7 protein. The expression profile of AtLACS6, AtLACS7, AtPEX5, and AtPEX7 revealed that AtLACS6 and 7 have distinct patterns of expression and we speculate that the possession of two targeting signals may be advantageous for the import of AtLACS7 when receptors may be limiting.     

Additive effects of herbivory,nectar robbing and seed predation on male and female fitness estimates of the host plant <Emphasis Type="Italic">Ipomopsis aggregata</Emphasis>

Many antagonistic species attack plants and consume specific plant parts. Understanding how these antagonists affect plant fitness individually and in combination is an important research focus in ecology and evolution. We examined the individual and combined effects of herbivory, nectar robbing, and pre-dispersal seed predation on male and female estimates of fitness in the host plant Ipomopsis aggregata. By examining the effects of antagonists on plant traits, we were able to tease apart the direct consumptive effects of antagonists versus the indirect effects mediated through changes in traits important to pollination. In a three-way factorial field experiment, we manipulated herbivory, nectar robbing, and seed predation. Herbivory and seed predation reduced some male and female fitness estimates, whereas plants tolerated the effects of robbing. The effects of herbivory, robbing, and seed predation were primarily additive, and we found little evidence for non-additive effects of multiple antagonists on plant reproduction. Herbivory affected plant reproduction through both direct consumptive effects and indirectly through changes in traits important to pollination (i.e., nectar and phenological traits). Conversely, seed predators primarily had direct consumptive effects on plants. Our results suggest that the effects of multiple antagonists on estimates of plant fitness can be additive, and investigating which traits respond to damage can provide insight into how antagonists shape plant performance.     

Fabrication of cell-containing gel modules to assemble modular tissue-engineered constructs [corrected

This paper describes a protocol to encapsulate cells in sub-millimeter-sized cylindrical collagen modules and to assemble these modules into a tissue-engineered construct within a continuous loop flow circuit. Modules are fabricated by gelling a solution of collagen, that contains suspended cells, within the lumen of a small-bore polyethylene tube. The tubing is then cut into short lengths using an automated cutter and gently vortexed to remove the cell-containing collagen modules from the tubing lumen. Modules are then randomly assembled into a modular construct by pipetting a suspension of modules into a larger tube that is positioned within a continuous flow circuit. A range of cylinder aspect ratios are achievable; therefore, this method could potentially be used to create short discs or, alternatively, long threads of soft gels, with or without encapsulated cells, for a variety of tissue-engineering applications. Module fabrication requires 1 d and assembly of a modular construct requires 2 h.     

Analysis of void volumes in proteins and application to stability of the p53 tumour suppressor protein

We have developed a new method for the analysis of voids in proteins (defined as empty cavities not accessible to solvent). This method combines analysis of individual discrete voids with analysis of packing quality. While these are different aspects of the same effect, they have traditionally been analysed using different approaches. The method has been applied to the calculation of total void volume and maximum void size in a non-redundant set of protein domains and has been used to examine correlations between thermal stability and void size. The tumour-suppressor protein p53 has then been compared with the non-redundant data set to determine whether its low thermal stability results from poor packing. We found that p53 has average packing, but the detrimental effects of some previously unexplained mutations to p53 observed in cancer can be explained by the creation of unusually large voids.     

In vitro induction of neoantigen-specific T cells in myelodysplastic syndrome,a disease with low mutational burden

Therapies that utilize immune checkpoint inhibition work by leveraging mutation-derived neoantigens and have shown greater clinical efficacy in tumors with higher mutational burden. Whether tumors with a low mutational burden are susceptible to neoantigen-targeted therapy has not been fully addressed. To examine the feasibility of neoantigen-specific adoptive T-cell therapy, the authors studied the T-cell response against somatic variants in five patients with myelodysplastic syndrome (MDS), a malignancy with a very low tumor mutational burden. DNA and RNA from tumor (CD34⁺) and normal (CD3⁺) cells isolated from the patients’ blood were sequenced to predict patient-specific MDS neopeptides. Neopeptides representing the somatic variants were used to induce and expand autologous T cells ex vivo, and these were systematically tested in killing assays to determine the proportion of neopeptides yielding neoantigen-specific T cells. The authors identified a total of 32 somatic variants (four to eight per patient) and found that 21 (66%) induced a peptide-specific T-cell response and 19 (59%) induced a T-cell response capable of killing autologous tumor cells. Of the 32 somatic variants, 11 (34%) induced a CD4⁺ response and 11 (34%) induced a CD8⁺ response that killed the tumor. These results indicate that in vitro induction of neoantigen-specific T cells is feasible for tumors with very low mutational burden and that this approach warrants investigation as a therapeutic option for such patients.     

Insect endosymbionts: manipulators of insect herbivore trophic interactions?

Throughout their evolutionary history, insects have formed multiple relationships with bacteria. Although many of these bacteria are pathogenic, with deleterious effects on the fitness of infected insects, there are also numerous examples of symbiotic bacteria that are harmless or even beneficial to their insect host. Symbiotic bacteria that form obligate or facultative associations with insects and that are located intracellularly in the host insect are known as endosymbionts. Endosymbiosis can be a strong driving force for evolution when the acquisition and maintenance of a microorganism by the insect host results in the formation of novel structures or changes in physiology and metabolism. The complex evolutionary dynamics of vertically transmitted symbiotic bacteria have led to distinctive symbiont genome characteristics that have profound effects on the phenotype of the host insect. Symbiotic bacteria are key players in insect–plant interactions influencing many aspects of insect ecology and playing a key role in shaping the diversification of many insect groups. In this review, we discuss the role of endosymbionts in manipulating insect herbivore trophic interactions focussing on their impact on plant utilisation patterns and parasitoid biology.     

Papillomavirus Genomes Associate with BRD4 to Replicate at Fragile Sites in the Host Genome

It has long been recognized that oncogenic viruses often integrate close to common fragile sites. The papillomavirus E2 protein, in complex with BRD4, tethers the viral genome to host chromatin to ensure persistent replication. Here, we map these targets to a number of large regions of the human genome and name them Persistent E2 and BRD4-Broad Localized Enrichments of Chromatin or PEB-BLOCs. PEB-BLOCs frequently contain deletions, have increased rates of asynchronous DNA replication, and are associated with many known common fragile sites. Cell specific fragile sites were mapped in human C-33 cervical cells by FANCD2 ChIP-chip, confirming the association with PEB-BLOCs. HPV-infected cells amplify viral DNA in nuclear replication foci and we show that these form adjacent to PEB-BLOCs. We propose that HPV replication, which hijacks host DNA damage responses, occurs adjacent to highly susceptible fragile sites, greatly increasing the chances of integration here, as is found in HPV-associated cancers.     

Substantial Metabolic Activity of Human Brown Adipose Tissue during Warm Conditions and Cold-Induced Lipolysis of Local Triglycerides

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