Macromolecular synthesis by yeasts under frozen conditions

Although viable fungi have been recovered from a wide variety of icy environments, their metabolic capabilities under frozen conditions are still largely unknown. We investigated basidiomycetous yeasts isolated from an Antarctic ice core and showed that after freezing at a relatively slow rate (0.8°C min⁻¹), the cells are excluded into veins of liquid at the triple junctions of ice crystals. These strains were capable of reproductive growth at −5°C under liquid conditions. Under frozen conditions, metabolic activity was assessed by measuring rates of [³H]leucine incorporation into the acid-insoluble macromolecular fraction, which decreased exponentially at temperatures between 15°C and −15°C and was inhibited by the protein synthesis inhibitor cycloheximide. Experiments at −5°C under frozen and liquid conditions revealed 2–3 orders of magnitude lower rates of endogenous metabolism in ice, likely due to the high salinity in the liquid fraction of the ice (equivalent of ≈ 1.4 mol l⁻¹ of NaCl at −5°C). The mesophile Saccharomyces cerevisae also incorporated [³H]leucine at −5°C and −15°C, indicating that this activity is not exclusive to cold-adapted microorganisms. The ability of yeast cells to incorporate amino acid substrates into macromolecules and remain metabolically active under these conditions has implications for understanding the survival of Eukarya in icy environments.     

A loop involving NRF2, miR-29b-1-5p and AKT,regulates cell fate of MDA-MB-231 triple-negative breast cancer cells

The present study shows that nuclear factor erythroid 2-related factor 2 (NRF2) and miR-29b-1-5p are two opposite forces which could regulate the fate of MDA-MB-231 cells, the most studied triple-negative breast cancer (TNBC) cell line. We show that NRF2 activation stimulates cell growth and markedly reduces reactive oxygen species (ROS) generation, whereas miR-29b-1-5p overexpression increases ROS generation and reduces cell proliferation. Moreover, NRF2 downregulates miR-29b-1-5p expression, whereas miR-29b-1-5p overexpression decreases p-AKT and p-NRF2. Furthermore, miR-29b-1-5p overexpression induces both inhibition of DNA N-methyltransferases (DNMT1, DNMT3A, and DNMT3B) expression and re-expression of HIN1, RASSF1A and CCND2. Conversely, NRF2 activation induces opposite effects. We also show that parthenolide, a naturally occurring small molecule, induces the expression of miR-29b-1-5p which could suppress NRF2 activation via AKT inhibition. Overall, this study uncovers a novel NRF2/miR-29b-1-5p/AKT regulatory loop that can regulate the fate (life/death) of MDA-MB-231 cells and suggests this loop as therapeutic target for TNBC.     

Vampirovibrio chlorellavorus draft genome sequence,annotation, and preliminary characterization of pathogenicity determinants

Vampirovibrio chlorellavorus is recognized as a pathogen of commercially‐relevant Chlorella species. Algal infection and total loss of productivity (biomass) often occurs when susceptible algal hosts are cultivated in outdoor open pond systems. The pathogenic life cycle of this bacterium has been inferred from laboratory and field observations, and corroborated in part by the genomic analyses for two Arizona isolates recovered from an open algal reactor. V. chlorellavorus predation has been reported to occur in geographically‐ and environmentally‐diverse conditions. Genomic analyses of these and additional field isolates is expected to reveal new information about the extent of ecological diversity and genes involved in host‐pathogen interactions. The draft genome sequences for two isolates of the predatory V. chlorellavorus (Cyanobacteria; Ca. Melainabacteria) from an outdoor cultivation system located in the Arizona Sonoran Desert were assembled and annotated. The genomes were sequenced and analyzed to identify genes (proteins) with predicted involvement in predation, infection, and cell death of Chlorella host species prioritized for biofuel production at sites identified as highly suitable for algal production in the southwestern USA. Genomic analyses identified several predicted genes encoding secreted proteins that are potentially involved in pathogenicity, and at least three apparently complete sets of virulence (Vir) genes, characteristic of the VirB‐VirD type system encoding the canonical VirB1‐11 and VirD4 proteins, respectively. Additional protein functions were predicted suggesting their involvement in quorum sensing and motility. The genomes of two previously uncharacterized V. chlorellavorus isolates reveal nucleotide and protein level divergence between each other, and a previously sequenced V. chlorellavorus genome. This new knowledge will enhance the fundamental understanding of trans‐kingdom interactions between a unique cosmopolitan cyanobacterial pathogen and its green microalgal host, of broad interest as a source of harvestable biomass for biofuels or bioproducts.     

Proteomic Signatures of Acquired Letrozole Resistance in Breast Cancer: Suppressed Estrogen Signaling and Increased Cell Motility and Invasiveness

Aromatase inhibitors, such as letrozole, have become the first-line treatment for postmenopausal women with estrogen-dependent breast cancer. However, acquired resistance remains a major clinical obstacle. Previous studies demonstrated constitutive activation of the MAPK signaling, overexpression of HER2, and down-regulation of aromatase and ERα in letrozole-resistant breast cancer cells. Given the complex signaling network involved in letrozole-refractory breast cancer and the lack of effective treatment for hormone resistance, further investigation of aromatase inhibitor resistance by a novel systems biology approach may reveal previously unconsidered molecular changes that could be utilized as therapeutic targets. This study was undertaken to characterize for the first time global proteomic alterations occurring in a letrozole-resistant cell line. A quantitative proteomic analysis of the whole cell lysates of LTLT-Ca (resistant) versus AC-1 cells (sensitive) was performed to identify significant protein expression changes. A total of 1743 proteins were identified and quantified, of which 411 were significantly up-regulated and 452 significantly down-regulated (p < 0.05, fold change > 1.20). Bioinformatics analysis revealed that acquired letrozole resistance is associated with a hormone-independent, more aggressive phenotype. LTLT-Ca cells exhibited 84% and 138% increase in migration and invasion compared with the control cells. The ROCK inhibitor partially abrogated the enhanced migration and invasion of the letrozole-resistant cells. Flow cytometric analyses also demonstrated an increase in vimentin and twist expression in letrozole-resistance cells, suggesting an onset of epithelial to mesenchymal transition (EMT). Moreover, targeted gene expression arrays confirmed a 28-fold and sixfold up-regulation of EGFR and HER2, respectively, whereas ERα and pS2 were dramatically reduced by 28-fold and 1100-fold, respectively. Taken together, our study revealed global proteomic signatures of a letrozole-resistant cell line associated with hormone independence, enhanced cell motility, EMT and the potential values of several altered proteins as novel prognostic markers or therapeutic targets for letrozole resistant breast cancer.Aromatase inhibitors (AIs)¹ have increasingly been used to treat ER positive breast cancer in postmenopausal women as adjuvant or neoadjuvant therapy (1, 2). AIs block estrogen production by inhibiting the aromatization reaction that converts androgens to estrogens, resulting in the remission of estrogen dependent breast tumors. However, acquired resistance occurs in the majority of patients after several years of AI treatment, and this may ultimately lead to eventual relapse of the disease (3, 4). Therefore it is necessary to better understand the resistance mechanisms to abrogate or delay the onset of AI resistance. Numerous studies have used in vitro and in vivo models to dissect the adaptive signaling events in the development of AI resistance in breast cancer (5, 6). The in vitro long term estrogen deprivation (LTED) model has been proposed to represent AI resistance in breast cancer that also showed cross-resistance to other hormonal treatment (7). However, the LTEDaro lines did not cluster with the AI-resistant lines (8). Alternatively, in vivo models using cells derived from mouse xenografts have been widely used to study the mechanism of AI resistance and potential therapeutic strategies (3, 9–11). Notably, ER expression levels were up-regulated in the LTED model (7) but down-regulated in the letrozole resistant breast cancer cells (12, 13).In in vitro experiments, it has been found that although MCF-7 and T47D (both ER+ breast cancer cell lines) express detectable levels of aromatase, the enzymatic activity is rather low for experimental studies of the action of aromatase inhibitors and subsequent resistance to AIs. It is recognized that the aromatase activity in MCF-7aro cells is significantly higher than that in typical breast cancer and surrounding adipose stromal cells. However, the aromatase activity in breast tumors can be elevated in situ by cytokines, cAMP, and cancer-promoting agents which stimulate protein kinase C activity (14–17). Thus these MCF-7 and AC1 cell lines are appropriate models for studying the balance between the androgenic and estrogenic effect in breast cancer as they express significant levels of AR and ER. Clinically, it has been observed that ∼66% of breast carcinomas contain aromatase (the rate-limiting enzyme responsible for estrogen biosynthesis), and the estrogen synthesized in situ has a role in stimulating the tumor (18, 19). In breast, ovarian, uterine, and prostate cancer, activation of PI.3/II leads to the overexpression of aromatase within the tissues themselves, and this has been associated with an increase in tumor growth (20, 21).In the mouse xenograft model established in Brodie''s laboratory, MCF-7 cells were stably transfected with the human aromatase gene and grown in ovariectomized female nude mice treated with letrozole for over 56 weeks (12, 22). Subsequent studies of these long-term letrozole treated (LTLT-Ca) cells isolated from these tumors confirmed the up-regulation of Her2/MAPK signaling cascade and the p160 coactivator, amplified in breast cancer 1 (AIB1), as an adaptive survival pathway (5, 12, 13, 23). Inhibition of MAPK led to reduced cell proliferation and restoration of ER expression, implicating the occurrence of crosstalk between ER and growth factor receptor signaling. Moreover, inhibition of Her2 restored the sensitivity of LTLT-Ca cells to letrozole (10, 23). In the genome-wide analysis of several hormone resistant cell lines, elevated DNA replication, recombination, repair function, cell cycle control, and the pyrimidine metabolism pathway were also found as an enhanced survival mechanism in the resistant cells (6, 7). Given the complex signaling network involved in AI refractory breast cancer and the lack of effective treatment for hormone resistance, further investigation of AI resistance by a global proteomics-based systems biology approach may reveal previously unconsidered molecular changes that could be used as therapeutic targets. Therefore, the objective of this study is to characterize global proteomic alterations occurring in the letrozole resistant cell line, originating from the Brodie laboratory (12).Here we have performed a quantitative proteomic analysis of the whole cell lysis samples of LTLT-Ca against the letrozole sensitive control cell line, AC-1, using a gel-free approach. To achieve relative quantitation of proteins we used a tandem mass tag labeling technique where each sample is triply labeled for analytical precision. Fractionation and nanoflow reverse phase HPLC were employed in combination with a high-resolution tandem mass spectrometer for peptide separation and identification. Identified protein markers were then analyzed by bioinformatics tools to gain insight into global adaptive signaling modulations as a result of acquired resistance to letrozole.     

Twist buckling behavior of arteries

Arteries are often subjected to torsion due to body movement and surgical procedures. While it is essential that arteries remain stable and patent under twisting loads, the stability of arteries under torsion is poorly understood. The goal of this work was to experimentally investigate the buckling behavior of arteries under torsion and to determine the critical buckling torque, the critical buckling twist angle, and the buckling shape. Porcine common carotid arteries were slowly twisted in vitro until buckling occurred while subjected to a constant axial stretch ratio (1.1, 1.3, 1.5 (in vivo level) and 1.7) and lumen pressure (20, 40, 70 and 100 mmHg). Upon buckling, the arteries snapped to form a kink. For a group of six arteries, the axial stretch ratio significantly affected the critical buckling torque (\(p<0.002\)) and the critical buckling twist angle (\(p<0.001\)). Lumen pressure also significantly affected the critical buckling torque (\(p<0.001\)) but had no significant effect on the critical twist angle (\(p=0.067\)). Convex material constants for a Fung strain energy function were determined and fit well with the axial force, lumen pressure, and torque data measured pre-buckling. The material constants are valid for axial stretch ratios, lumen pressures, and rotation angles of 1.3–1.5, 20–100 mmHg, and 0–270\(^\circ \), respectively. The current study elucidates the buckling behavior of arteries under torsion and provides new insight into mechanical instability of blood vessels.     

Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content, and rearrangements revealed by next generation sequencing

The complete plastid genome sequence of the American cranberry (Vaccinium macrocarpon Ait.) was reconstructed using next-generation sequencing data by in silico procedures. We used Roche 454 shotgun sequence data to isolate cranberry plastid-specific sequences of “HyRed” via homology comparisons with complete sequences from several species available at the National Center for Biotechnology Information database. Eleven cranberry plastid contigs were selected for the construction of the plastid genome-based homologies and on raw reads flowing through contigs and connection information. We assembled and annotated a cranberry plastid genome (82,284 reads; 185x coverage) with a length of 176 kb and the typical structure found in plants, but with several structural rearrangements in the large single-copy region when compared to other plastid asterid genomes. To evaluate the reliability of the sequence data, phylogenetic analysis of 30 species outside the order Ericales (with 54 genes) showed Vaccinium inside the clade Asteridae, as reported in other studies using single genes. The cranberry plastid genome sequence will allow the accumulation of critical data useful for breeding and a suite of other genetic studies.     

Gleevec,an Abl Family Inhibitor,Produces a Profound Change in Cell Shape and Migration

The issue of how contractility and adhesion are related to cell shape and migration pattern remains largely unresolved. In this paper we report that Gleevec (Imatinib), an Abl family kinase inhibitor, produces a profound change in the shape and migration of rat bladder tumor cells (NBTII) plated on collagen-coated substrates. Cells treated with Gleevec adopt a highly spread D-shape and migrate more rapidly with greater persistence. Accompanying this more spread state is an increase in integrin-mediated adhesion coupled with increases in the size and number of discrete adhesions. In addition, both total internal reflection fluorescence microscopy (TIRFM) and interference reflection microscopy (IRM) revealed a band of small punctate adhesions with rapid turnover near the cell leading margin. These changes led to an increase in global cell-substrate adhesion strength, as assessed by laminar flow experiments. Gleevec-treated cells have greater RhoA activity which, via myosin activation, led to an increase in the magnitude of total traction force applied to the substrate. These chemical and physical alterations upon Gleevec treatment produce the dramatic change in morphology and migration that is observed.     

The Epitope of Monoclonal Antibodies Blocking Erythrocyte Invasion by Plasmodium falciparum Map to The Dimerization and Receptor Glycan Binding Sites of EBA-175

The malaria parasite, Plasmodium falciparum, and related parasites use a variety of proteins with Duffy-Binding Like (DBL) domains to bind glycoproteins on the surface of host cells. Among these proteins, the 175 kDa erythrocyte binding antigen, EBA-175, specifically binds to glycophorin A on the surface of human erythrocytes during the process of merozoite invasion. The domain responsible for glycophorin A binding was identified as region II (RII) which contains two DBL domains, F1 and F2. The crystal structure of this region revealed a dimer that is presumed to represent the glycophorin A binding conformation as sialic acid binding sites and large cavities are observed at the dimer interface. The dimer interface is largely composed of two loops from within each monomer, identified as the F1 and F2 β-fingers that contact depressions in the opposing monomers in a similar manner. Previous studies have identified a panel of five monoclonal antibodies (mAbs) termed R215 to R218 and R256 that bind to RII and inhibit invasion of erythrocytes to varying extents. In this study, we predict the F2 β-finger region as the conformational epitope for mAbs, R215, R217, and R256, and confirm binding for the most effective blocking mAb R217 and R215 to a synthetic peptide mimic of the F2 β-finger. Localization of the epitope to the dimerization and glycan binding sites of EBA-175 RII and site-directed mutagenesis within the predicted epitope are consistent with R215 and R217 blocking erythrocyte invasion by Plasmodium falciparum by preventing formation of the EBA-175– glycophorin A complex.