Polar transmembrane domains target proteins to the interior of the yeast vacuole

Membrane proteins transported to the yeast vacuole can have two fates. Some reach the outer vacuolar membrane, whereas others enter internal vesicles, which form in late endosomes, and are ultimately degraded. The vacuolar SNAREs Nyv1p and Vam3p avoid this fate by using the AP-3-dependent pathway, which bypasses late endosomes, but the endosomal SNARE Pep12p must avoid it more directly. Deletion analysis revealed no cytoplasmic sequences necessary to prevent the internalization of Pep12p in endosomes. However, introduction of acidic residues into the cytoplasmic half of the transmembrane domain created a dominant internalization signal. In other contexts, this same feature diverted proteins from the Golgi to endosomes and slowed their exit from the endoplasmic reticulum. The more modestly polar transmembrane domains of Sec12p and Ufe1p, which normally serve to hold these proteins in the endoplasmic reticulum, also cause Pep12p to be internalized, as does that of the vacuolar protein Cps1p. It seems that quality control mechanisms recognize polar transmembrane domains at multiple points in the secretory and endocytic pathways and in endosomes sort proteins for subsequent destruction in the vacuole. These mechanisms may minimize the damaging effects of abnormally exposed polar residues while being exploited for the localization of some normal proteins.     

Ability to Generate Patient-Derived Breast Cancer Xenografts Is Enhanced in Chemoresistant Disease and Predicts Poor Patient Outcomes

BackgroundBreast cancer patients who are resistant to neoadjuvant chemotherapy (NeoCT) have a poor prognosis. There is a pressing need to develop in vivo models of chemo resistant tumors to test novel therapeutics. We hypothesized that patient-derived breast cancer xenografts (BCXs) from chemo- naïve and chemotherapy-exposed tumors can provide high fidelity in vivo models for chemoresistant breast cancers.MethodsPatient tumors and BCXs were characterized with short tandem repeat DNA fingerprinting, reverse phase protein arrays, molecular inversion probe arrays, and next generation sequencing.ResultsForty-eight breast cancers (24 post-chemotherapy, 24 chemo-naïve) were implanted and 13 BCXs were established (27%). BCX engraftment was higher in TNBC compared to hormone-receptor positive cancer (53.8% vs. 15.6%, p = 0.02), in tumors from patients who received NeoCT (41.7% vs. 8.3%, p = 0.02), and in patients who had progressive disease on NeoCT (85.7% vs. 29.4%, p = 0.02). Twelve patients developed metastases after surgery; in five, BCXs developed before distant relapse. Patients whose tumors developed BCXs had a lower recurrence-free survival (p = 0.015) and overall survival (p<0.001). Genomic losses and gains could be detected in the BCX, and three models demonstrated a transformation to induce mouse tumors. However, overall, somatic mutation profiles including potential drivers were maintained upon implantation and serial passaging. One BCX model was cultured in vitro and re-implanted, maintaining its genomic profile.ConclusionsBCXs can be established from clinically aggressive breast cancers, especially in TNBC patients with poor response to NeoCT. Future studies will determine the potential of in vivo models for identification of genotype-phenotype correlations and individualization of treatment.     

Contact-Inhibited Revertant Cell Lines Isolated from Simian Virus 40-Transformed Cells III. Concanavalin A-Selected Revertant Cells

Contact-inhibited variants have been isolated by treatment of simian virus 40 (SV40)-transformed Balb/c 3T3 cells (SVT2) with the plant lectin concanavalin A. These con A revertant cells exhibit the following properties: (i) they resemble 3T3 cells morphologically and grow to saturation densities which are similar to that of 3T3 cells; (ii) they synthesize the SV40-specific T antigen and yield infectious virus after fusion with permissive monkey cells; (iii) they contain a high sialic acid content similar to that of 3T3 cells and not to that of SVT2 cells; sialic acid composition was found to be independent of serum concentration; (iv) they contain more chromosomes with the average number in the tetraploid range than the SVT2 cells from which they were derived; and (v) SVT2 and revertant cells, confluent or subconfluent, produce more collagen than Balb/3T3 cells. The relationship of surface membrane properties to contact inhibition of growth and the mechanisms for generating revertant cells are discussed.     

Staphylococci in Competition: II. Effect of Total Numbers and Proportion of Staphylococci in Mixed Cultures on Growth in Artificial Culture Medium

In studies carried on in bacteriological media with selected cultures, definite repressive effects were noted on the growth of the Staphylococcus population by a mixture of saprophytic, psychrophilic bacterial species. This repressive effect became more pronounced as the relative proportion of the bacterial population which was staphylococcal became smaller. A varied saprophytic bacterial flora of some numbers apparently would offer definite protection to foods through repression of staphylococcal growth and by rendering the food inedible before the rise of appreciable numbers of staphylococci. It would appear that at the optimal temperature for staphylococcal growth, staphylococci could multiply rapidly in the mixed population due to the comparative shortness of the generation time of this species and because of the lengthened lag phase of the saprophytic bacterial species at this elevated temperature, especially when only cultures having psychrophilic characteristics were present. This temperature is substantially above that encountered in practical experience. With the passage of time, the staphylococcal population was completely overgrown by the saprohytes present. This effect might be eliminated in the presence of psychrophilic and mesophilic, saprophytic species. The repressive effect of competition by saprophytic, psychrophilic organisms is extremely effective up to room temperature on the staphylococcal population. Even when significant staphylococcal populations were achieved in the artificial media, such tremendous numbers of saprophytes were obtained either earlier or at the same time so that a frozen food containing this population would be organoleptically unacceptable due to the degradative action of enzymes from the saprophytic psychrophile population.     

The 1.14 A crystal structure of yeast cytosine deaminase: evolution of nucleotide salvage enzymes and implications for genetic chemotherapy

Cytosine deaminase (CD) catalyzes the deamination of cytosine and is only present in prokaryotes and fungi, where it is a member of the pyrimidine salvage pathway. The enzyme is of interest both for antimicrobial drug design and gene therapy applications against tumors. The structure of Saccharomyces cerevisiae CD has been determined in the presence and absence of a mechanism-based inhibitor, at 1.14 and 1.43 A resolution, respectively. The enzyme forms an alpha/beta fold similar to bacterial cytidine deaminase, but with no similarity to the alpha/beta barrel fold used by bacterial cytosine deaminase or mammalian adenosine deaminase. The structures observed for bacterial, fungal, and mammalian nucleic acid deaminases represent an example of the parallel evolution of two unique protein folds to carry out the same reaction on a diverse array of substrates.     

Long‐term growth‐increment chronologies reveal diverse influences of climate forcing on freshwater and forest biota in the Pacific Northwest

Analyses of how organisms are likely to respond to a changing climate have focused largely on the direct effects of warming temperatures, though changes in other variables may also be important, particularly the amount and timing of precipitation. Here, we develop a network of eight growth‐increment width chronologies for freshwater mussel species in the Pacific Northwest, United States and integrate them with tree‐ring data to evaluate how terrestrial and aquatic indicators respond to hydroclimatic variability, including river discharge and precipitation. Annual discharge averaged across water years (October 1–September 30) was highly synchronous among river systems and imparted a coherent pattern among mussel chronologies. The leading principal component of the five longest mussel chronologies (1982–2003; PC1_mussel) accounted for 47% of the dataset variability and negatively correlated with the leading principal component of river discharge (PC1_discharge; r = ?0.88; P < 0.0001). PC1_mussel and PC1_discharge were closely linked to regional wintertime precipitation patterns across the Pacific Northwest, the season in which the vast majority of annual precipitation arrives. Mussel growth was also indirectly related to tree radial growth, though the nature of the relationships varied across the landscape. Negative correlations occurred in forests where tree growth tends to be limited by drought while positive correlations occurred in forests where tree growth tends to be limited by deep or lingering snowpack. Overall, this diverse assemblage of chronologies illustrates the importance of winter precipitation to terrestrial and freshwater ecosystems and suggests that a complexity of climate responses must be considered when estimating the biological impacts of climate variability and change.     

Dietary polyunsaturated fatty acids (C18:2 omega6 and C18:3 omega3) do not suppress hepatic lipogenesis

Omega 3 polyunsaturated fatty acids are promoted as beneficial in the prevention of metabolic and cardiovascular diseases. In general, dietary omega 3 fatty acids are derived from plant sources as linolenic acid (LNA, C18:3 omega3) the precursor to eicosapentaenoic acid (EPA, C20:5 omega3) and docosahexaenoic acid (DHA, C22:6 omega3). However, it remains unclear if the polyunsaturated fatty acid (PUFA) LNA can provide the same health benefits as the very long chain highly unsaturated fatty acids (HUFA) EPA and DHA generally derived from oily fish. In this study, mice were fed synthetic diets containing lard (low in PUFA and HUFA), canola oil (to supply PUFA), or a mixture of menhaden and arasco (fish and fungal) oils (to supply HUFA) for 8 weeks. The diets were neither high in calories nor fat, which was supplied at 6%. The lard and canola oil diets resulted in high levels of hepatic triglycerides and cholesterol and elevation of lipogenic gene expression. By comparison livers from mice fed the fish/fungal oil diet had low levels of lipid accumulation and more closely resembled livers from mice fed standard laboratory chow. SREBP1c and PPARgamma gene and protein expression were high in livers of animals fed diets containing lard or canola oil compared with fish/fungal oil. Hepatic fatty acid analyses indicated that dietary PUFA were efficiently converted to HUFA regardless of source. Therefore, differences in hepatic lipid levels and gene expression between dietary groups were due to exogenous fatty acid supplied rather than endogenous pools. These results have important implications for understanding the regulation of hepatic lipogenesis by dietary fatty acids.     

Effect of IL-6 trans-signaling on the pro-remodeling phenotype of airway smooth muscle

Increased levels of IL-6 are documented in asthma, but its contribution to the pathology is unknown. Asthma is characterized by airway wall thickening due to increased extracellular matrix deposition, inflammation, angiogenesis, and airway smooth muscle (ASM) mass. IL-6 binds to a specific membrane-bound receptor, IL-6 receptor-alpha (mIL-6Ralpha), and subsequently to the signaling protein gp130. Alternatively, IL-6 can bind to soluble IL-6 recpetor-alpha (sIL-6Ralpha) to stimulate membrane receptor-deficient cells, a process called trans-signaling. We discovered that primary human ASM cells do not express mIL-6Ralpha and, therefore, investigated the effect of IL-6 trans-signaling on the pro-remodeling phenotype of ASM. ASM required sIL-6Ralpha to activate signal transducer and activator 3, with no differences observed between cells from asthmatic subjects compared with controls. Further analysis revealed that IL-6 alone or with sIL-6Ralpha did not induce release of matrix-stimulating factors (including connective tissue growth factor, fibronectin, or integrins) and had no effect on mast cell adhesion to ASM or ASM proliferation. However, in the presence of sIL-6Ralpha, IL-6 increased eotaxin and VEGF release and may thereby contribute to local inflammation and vessel expansion in airway walls of asthmatic subjects. As levels of sIL-6Ralpha are increased in asthma, this demonstration of IL-6 trans-signaling in ASM has relevance to the development of airway remodeling.     

Human Fatty Acid Transport Protein 2a/Very Long Chain Acyl-CoA Synthetase 1 (FATP2a/Acsvl1) Has a Preference in Mediating the Channeling of Exogenous n-3 Fatty Acids into Phosphatidylinositol

The trafficking of fatty acids across the membrane and into downstream metabolic pathways requires their activation to CoA thioesters. Members of the fatty acid transport protein/very long chain acyl-CoA synthetase (FATP/Acsvl) family are emerging as key players in the trafficking of exogenous fatty acids into the cell and in intracellular fatty acid homeostasis. We have expressed two naturally occurring splice variants of human FATP2 (Acsvl1) in yeast and 293T-REx cells and addressed their roles in fatty acid transport, activation, and intracellular trafficking. Although both forms (FATP2a (M_r 70,000) and FATP2b (M_r 65,000 and lacking exon3, which encodes part of the ATP binding site)) were functional in fatty acid import, only FATP2a had acyl-CoA synthetase activity, with an apparent preference toward very long chain fatty acids. To further address the roles of FATP2a or FATP2b in fatty acid uptake and activation, LC-MS/MS was used to separate and quantify different acyl-CoA species (C14–C24) and to monitor the trafficking of different classes of exogenous fatty acids into intracellular acyl-CoA pools in 293T-REx cells expressing either isoform. The use of stable isotopically labeled fatty acids demonstrated FATP2a is involved in the uptake and activation of exogenous fatty acids, with a preference toward n-3 fatty acids (C18:3 and C22:6). Using the same cells expressing FATP2a or FATP2b, electrospray ionization/MS was used to follow the trafficking of stable isotopically labeled n-3 fatty acids into phosphatidylcholine and phosphatidylinositol. The expression of FATP2a resulted in the trafficking of C18:3-CoA and C22:6-CoA into both phosphatidylcholine and phosphatidylinositol but with a distinct preference for phosphatidylinositol. Collectively these data demonstrate FATP2a functions in fatty acid transport and activation and provides specificity toward n-3 fatty acids in which the corresponding n-3 acyl-CoAs are preferentially trafficked into acyl-CoA pools destined for phosphatidylinositol incorporation.     

Effect of soil compaction on barley (Hordeum vulgare L.) growth: I. Possible role for ABA as a root-sourced chemical signal

Wild-type (Steptoe) and abscisic acid (ABA)-deficient mutant(Az34) genotypes of barley were grown in compacted soil to examinethe potential role of ABA as a root-to-shoot signal. Root andshoot growth and leaf conductance were all reduced when plantswere grown in compacted soil with a bulk density of 1.7g cm^–3,relative to uncompacted control plants (1.1 g cm^–3. Theseeffects occurred in the absence of detectable changes in leafwater status or foliar abscisic acid (ABA) content. Analysisof Steptoe and Az34 xylem sap showed that the ABA concentrationwas greatly increased at 6 d after emergence (6 DAE) when seedlingswere grown in compacted soil (1.7 g cm^–3); however, ABAconcentrations were never as high in the mutant as in the wildtype. The increase in xylem sap ABA concentration observed athigh bulk density was closely correlated with reductions inleaf conductance, but not leaf area. These increases were transitory,and xylem sap ABA concentrations subsequently decreased towardsthe control level by 18 DAE in both genotypes. The ABA-deficient mutant, Az34, produced a much lower leaf areathan Steptoe at a bulk density of 1.6 g cm^–3. Examinationof epidermal characteristics indicates that this effect resultedmainly from reductions in cell expansion rather than cell division,suggesting that the higher ABA concentrations detected in xylemsap from the wild-type Steptoe may have exerted a positive rolein maintaining leaf expansion in this treatment. The possibleinvolvement of ABA as a root-to-shoot signal mediating the effectsof compaction stress is discussed. Key words: Soil compaction, bulk density, ABA, ABA-deficient mutant, leaf growth