The glucose‐deprivation network counteracts lapatinib‐induced toxicity in resistant ErbB2‐positive breast cancer cells

Dynamic interactions between intracellular networks regulate cellular homeostasis and responses to perturbations. Targeted therapy is aimed at perturbing oncogene addiction pathways in cancer, however, development of acquired resistance to these drugs is a significant clinical problem. A network‐based computational analysis of global gene expression data from matched sensitive and acquired drug‐resistant cells to lapatinib, an EGFR/ErbB2 inhibitor, revealed an increased expression of the glucose deprivation response network, including glucagon signaling, glucose uptake, gluconeogenesis and unfolded protein response in the resistant cells. Importantly, the glucose deprivation response markers correlated significantly with high clinical relapse rates in ErbB2‐positive breast cancer patients. Further, forcing drug‐sensitive cells into glucose deprivation rendered them more resistant to lapatinib. Using a chemical genomics bioinformatics mining of the CMAP database, we identified drugs that specifically target the glucose deprivation response networks to overcome the resistant phenotype and reduced survival of resistant cells. This study implicates the chronic activation of cellular compensatory networks in response to targeted therapy and suggests novel combinations targeting signaling and metabolic networks in tumors with acquired resistance.     

Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases

Engineered polyketide synthases (PKSs) are promising synthetic biology platforms for the production of chemicals with diverse applications. The dehydratase (DH) domain within modular type I PKSs generates an α,β-unsaturated bond in nascent polyketide intermediates through a dehydration reaction. Several crystal structures of DH domains have been solved, providing important structural insights into substrate selection and dehydration. Here, we present two DH domain structures from two chemically diverse PKSs. The first DH domain, isolated from the third module in the borrelidin PKS, is specific towards a trans-cyclopentane-carboxylate-containing polyketide substrate. The second DH domain, isolated from the first module in the fluvirucin B₁ PKS, accepts an amide-containing polyketide intermediate. Sequence-structure analysis of these domains, in addition to previously published DH structures, display many significant similarities and key differences pertaining to substrate selection. The two major differences between BorA DH M3, FluA DH M1 and other DH domains are found in regions of unmodeled residues or residues containing high B-factors. These two regions are located between α3–β11 and β7–α2. From the catalytic Asp located in α3 to a conserved Pro in β11, the residues between them form part of the bottom of the substrate-binding cavity responsible for binding to acyl-ACP intermediates.

     

The depth of Sooty Shearwater Ardenna grisea burrows varies with habitat and increases with competition for space

The Sooty Shearwater Ardenna grisea, an abundant but declining petrel, is one of many seabird species that construct breeding burrows, presumably because these confer protection from predators and the elements. Little is known about the causes of variation in Sooty Shearwater burrow architecture, which can differ markedly both within and between breeding sites. We hypothesize that burrow architecture varies in response to habitat type and competition for space. To address these hypotheses, we recorded Sooty Shearwater burrow dimensions on Kidney Island, the largest Sooty Shearwater colony in the Falkland Islands, South Atlantic, and modelled these as functions of burrow density (a proxy for competition) and habitat indices. Our models suggest that Sooty Shearwaters burrow further underground in response to competition for breeding space, and that soil underlying dense tussac grass Poa flabellata is more easily excavated than other substrates, indicating how vegetation restoration could aid the conservation of this species.     

Detection of large cDNA inserts within crude lambda gt11 lysates: a rapid and sensitive method

A method is presented for the isolation of bacteriophage lambda DNA and the rapid identification of large cDNA inserts within crude phage lysates. The primary screening of a lambda gt11 cDNA library with a 32P-radiolabeled cDNA probe yielded 21 putative positive clones. A phage "spot-blot" analysis was employed to quickly screen these potential recombinants. This eliminated 9 of the 21 clones as the result of false positive signals. The remaining 12 recombinant phage were amplified on agarose-based media, and phage DNA was isolated using a modified plate lysate procedure. The DNA thus obtained from these crude lysates could be easily digested with EcoRI and examined by Southern blot analysis. The resulting blot was hybridized with the same cDNA probe used in the initial screening of the library. Thus, two clones harboring the longest cDNA insert were identified from a mixed phage population and were subsequently plaque purified. The procedure is rapid, sensitive, reproducible, inexpensive and allows the processing of several clones at once without sacrificing the quality or yields of the DNA preparation. Furthermore, the method obviates the need for plaque purifying all the positives obtained from the initial screening of a cDNA library.     

Life history,distribution and molecular phylogenetics of the Upward-Mouth Spikefish Atrophacanthus japonicus (Teleostei: Tetraodontiformes: Triacanthodidae)

Ninety-six juvenile specimens (37–54 mm standard length; L_S) of the rarely collected Upward-Mouth Spikefish Atrophacanthus japonicus (Triacanthodidae) were obtained from the stomachs of three Yellowfin Tuna Thunnus albacares collected off Guam in the Mariana Islands in the central Pacific Ocean. These specimens extend the range of A. japonicus eastward into Oceania. We review the systematic characters of the monotypic genus Atrophacanthus and present colour photographs of freshly collected specimens. The diet of the juvenile specimens of A. japonicus consisted of thecosome pteropods and foraminiferans. We present a range map of A. japonicus based on all known specimens and show that specimen size is related to whether specimens were collected in the pelagic zone or on the bottom. Our results support that, compared to all other Triacanthodidae, A. japonicus has an unusually extended pelagic larval and juvenile period, up to 54 mm L_S, before settling to the bottom as adults. Lastly, we provide a multilocus phylogeny addressing the phylogenetic placement of Atrophacanthus based on eight of 11 triacanthodid genera and six genetic markers. Our results reveal that Atrophacanthus is the sister group of Macrorhamphosodes and they provide new insights about the evolutionary history of the family.     

High Conformational Variability in the GluK2 Kainate Receptor Ligand-Binding Domain

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Extensive gaps and biases in our knowledge of a well‐known fauna: implications for integrating biological traits into macroecology

Aim Ecologists seeking to describe patterns at ever larger scales require compilations of data on the global abundance and distribution of species. Comparable compilations of biological data are needed to elucidate the mechanisms behind these patterns, but have received far less attention. We assess the availability of biological data across an entire assemblage: the well‐documented demersal marine fauna of the United Kingdom. We also test whether data availability for a species depends on its taxonomic group, maximum body size, the number of times it has been recorded in a global biogeographic database, or its commercial and conservation importance. Location Seas of the United Kingdom. Methods We defined a demersal marine fauna of 973 species from 15 phyla and 40 classes using five extensive surveys around the British Isles. We then quantified the availability of data on eight key biological traits (termed biological knowledge) for each species from online databases. Relationships between biological knowledge and our predictors were tested with generalized linear models. Results Full data on eight fundamental biological traits exist for only 9% (n= 88) of the UK demersal marine fauna, and 20% of species completely lack data. Clear trends in our knowledge exist: fish (median biological knowledge score = six traits) are much better known than invertebrates (one trait). Biological knowledge increases with biogeographic knowledge and (to a lesser extent) with body size, and is greater in species that are commercially exploited or of conservation concern. Main conclusions Our analysis reveals deep ignorance of the basic biology of a well‐studied fauna, highlighting the need for far greater efforts to compile biological trait data. Clear biases in our knowledge, relating to how well sampled or ‘important’ species are suggests that caution is required in extrapolating small subsets of biologically well‐known species to ecosystem‐level studies.     

LAMINATED MEMBRANE SURFACE AND OSMIOPHILIC INCLUSIONS IN AVIAN LUNG EPITHELIUM

A study of the fine structure of the avian lung revealed the presence of a unique laminated membrane surface and associated osmiophilic inclusions in epithelial cells of the tertiary bronchi and atria. These structures were not found in the air-capillary epithelium. Each lamination of the membrane surface had the appearance and dimensions of the unit membrane. It is suggested that the laminated membrane surface is associated with the formation of the osmiophilic inclusions and that these inclusions compare with those described in mammalian alveolar epithelium. It is further suggested that the laminated membrane surface is lipoprotein or phospholipid in composition and is responsible for the surface-tension-reducing properties of avian lung extracts.