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The consensus linear view of G1/S regulation has served the research community for many years. Recent data indicate considerable heterogeneity in cancer cycles as controlled by distinct cyclin-dependent kinase (CDK) and cyclin complexes. Adaptation and unexpected dependencies reveal emerging themes that support a malleable model for cancer cell division. The growing complexity of the cell cycle offers challenges and opportunities in rationally targeting proliferative control. In the commonly accepted paradigm for control of the mammalian cell cycle, sequential cyclin-dependent kinase (CDK) and cyclin activities drive the orderly transition from G1 to S phase. However, recent studies using different technological approaches and examining a broad range of cancer cell types are challenging this established paradigm. An alternative model is evolving in which cell cycles utilize different drivers and take different trajectories through the G1/S transition. We are discovering that cancer cells in particular can adapt their drivers and trajectories, which has important implications for antiproliferative therapies. These studies have helped to refine an understanding of how CDK inhibition impinges on proliferation and have significance for understanding fundamental features of cell biology and cancer. [ABSTRACT FROM AUTHOR]

Ability to promote completion of mitotic cycling of adult mammalian cardiomyocytes remains an intractable and vexing challenge, despite being one of the most sought after 'holy grails' of cardiovascular research. While some of the struggle is attributable to adult cardiomyocytes themselves that are notoriously post-mitotic, another contributory factor rests with difficulty in definitive tracking of adult cardiomyocyte cell cycle and lack of rigorous measures to track proliferation in situ. This review summarizes past, present, and future directions to promote adult mammalian cardiomyocyte cell cycle progression, proliferation, and renewal. Establishing relationship(s) between cardiomyocyte cell cycle progression and cellular biological properties is sorely needed to understand the mechanistic basis for cardiomyocyte cell cycle withdrawal to enhance cardiomyocyte cell cycle progression and mitosis. Adult mammalian cardiomyocytes are remarkably refractory to completion of cell cycle progression through mitosis. Despite ongoing study for decades, progress to promote adult mammalian cardiomyocyte cell cycle completion has been frustratingly ineffective. Fundamental biological differences exist between adult mammalian cardiomyocytes versus those derived from neonatal mice or lower vertebrates, such as zebrafish, that both possess relatively immature phonotypes. Studies reporting cardiomyocyte proliferation often lack definitive proof of authentic cardiomyocyte mitotic activity due to methodologies misrepresented as completion of cell cycle progression. Two major points of cell cycle withdrawal for adult mammalian cardiomyocytes are the restriction point (R-point) and acquisition of higher level ploidy through multinucleation (polyploidy). [ABSTRACT FROM AUTHOR]

Cyclic AMP (cAMP) is an important second messenger that mediates various biological functions in both prokaryotes and eukaryotes. Due to the ever increasing significance in studying the function and modulation of cAMP-based signaling, it is important to develop a protein-based biosensor that reports the cAMP mediated gene expression. Based on a synthetic transgene approach, an artificial mammalian transactivator was developed by fusing a transcriptional regulatory element cAMP receptor protein (CRP) of Escherichia coli to the VP16 transactivation domain of Herpes simplex virus in a mammalian expression vector (pLA1) that activates CRP specific operator site present in a chimeric promoter (O CRP - PhCMV min - Luciferase) in a concentration dependent manner in mammalian cells. Our results reveal that the engineered transactivator report the gene expression mediated by cAMP directly in mammalian cells and this cAMP reporter system works irrespective of Protein kinase A (PKA) - cyclic AMP response element binding protein (CREB) - cyclic AMP response element (CRE) signaling since the luciferase activity mediated by synthetic gene construct is seen even in the presence of PKA inhibitor H-89 (derived from H-8 (N-[2-(methylamino) ethyl]-5-isoquinoline-sulfonamide). Furthermore this synthetic transcription factor plays a significant role in reporting and mediating cAMP signaling in tumorigenic cells which possess an aberrant cAMP signaling due to PKA and CREB mutations. [ABSTRACT FROM AUTHOR]

Abstract This work presents the development and validation of a quantitative HILIC UHPLC-ESI-QTOF-MS/MS method for amino acids combined with untargeted metabolic profiling of human corneal epithelial (HCE) cells after treatment with ionic liquids. The work included a preliminary metabotoxicity screening of 14 different ionic liquids, of which 9 carefully selected ionic liquids were chosen for a metabolomics study. This study is focused on the correlation between the toxicity of the ionic liquids and their metabolic profiles. The method development included the comparison of different MS/MS acquisition modes. A sequential window acquisition of all theoretical fragment ion mass spectra (SWATH) method with variable Q1 window widths and narrow Q1 target windows of 5 Da for most of the amino acids was selected as the optimal acquisition mode. Due to the absence of a true blank matrix, 13C,15N-isotopically labelled amino acids were utilized as surrogate calibrants, instead of proteinogenic amino acids. Partial least squares (PLS) analysis of the median effective concentrations (EC 50) of 9 selected ionic liquids showed a correlation with their metabolic profile measured by the untargeted screening. Graphical abstract fx1 Highlights • UHPLC-ESI-MS/MS method for quantitative amino acids analysis in cells developed. • Data-independent acquisition allows simultaneous untargeted metabolic profiling. • PLS reveals a correlation between metabolic profiles and toxicity of ILs. • The most toxic ILs tested were [P 4441 ][OAc], [P 14444 ][OAc] and [P 14444 ]Cl. • LC-MS metabolic profiling seems to be a useful strategy to classify the toxicity of ILs. [ABSTRACT FROM AUTHOR]

Abstract The reaction of 5,5′-dithiobis(2-nitrobenzoate), DTNB, with hemoglobin sulfhydryl groups is linked to three negatively contributing Bohr effect groups: His2β is present in all avian hemoglobins but absent in some mammalian hemoglobins; His77β and His143β are absent in avian but present in nearly all mammalian hemoglobins. To probe the consequences of these differences, we determined the influence of inositol hexakisphosphate (inositol-P 6) on the DTNB affinities of avian and mammalian carbonmonoxyhemoglobins. Inositol-P 6 decreases by two orders of magnitude the DTNB affinity of guinea pig hemoglobin, which has His2β and the R2 quaternary structure. It decreases, or has no effect on, the DTNB affinities of hemoglobins that have His2β and whose structures lie along the R2 ⇌ R quaternary equilibrium. Finally, inositol-P 6 increases by one to two orders of magnitude the DTNB affinities of hemoglobins that lack His2β. Thus His2β, DTNB and inositol-P 6 , in combination, distinguish the R2 from the R quaternary structure. Graphical abstract Unlabelled Image Highlights • Guinea pig Hb has the R2 quaternary structure and His2β; and inositol-P 6 decreases its affinity for Ellman's reagent. • Ungulate and cat Hbs have R quaternary structure, lack His2β, and inositol-P 6 increases their affinity for Ellman's reagent. • Human and dog Hb have His2β and structures between R2 and R. Inositol-P 6 has no effect on their Ellman's reagent affinities. • Avian Hbs have His2β and structures between R2 and R. Inositol-P 6 has no effect on their Ellman's reagent affinities. • Chicken major Hb has His2β. Inositol-P 6 decreases its Ellman's reagent affinity; it has the R2 quaternary structure. [ABSTRACT FROM AUTHOR]

Highlights • DNA/PEI complexes formed immediately and underwent aggregation. • 1E+10 complexes/mL with 300-nm sizes were found after DNA/PEI complex formation. • 250 complexes per cell and aggregates were found at the time of transfection. • Morphology and composition of complexes were analyzed by EM. • Complex aggregates were required to enhance HEK 293 transient transfection. Abstract Polyethyleneimine (PEI) has been used extensively for transient gene expression (TGE) in mammalian cell cultures. However, the relationship between DNA/PEI complex preparation and their biological activity has not been fully established. Here, a systematic study of DNA/PEI complexes, their physicochemical properties during formation and their transfection efficiency was performed on a virus-like particle (VLP) production platform. The same chemically defined cell culture medium for DNA/PEI complex formation was used as an alternative to simple ionic solutions to minimize changes in complex properties during transfection. Upon formation, an initial concentration of 1E + 10 DNA/PEI complexes/mL underwent partial aggregation with an average size of 300 nm. The participation of NaCl ions in the evolution of complexes was analyzed by X-ray spectroscopy, stressing the relevance of complexing media composition in TGE strategies. After 15 min incubation, 250 complexes plus aggregates per cell were estimated at the time of transfection. Such heterogeneous preparations cannot be easily characterized; subsequently, nanoparticle tracking analysis (NTA) and cryo-electron microscopy were combined to achieve a complete picture of the preparation. Finally, the contribution of each DNA/PEI complex subpopulation was tested by drug inhibition endocytosis. Interestingly, all complexes delivered DNA efficiently and high size aggregates, which enter through macropinocytosis, when inhibited presented a major contribution to transfection efficiency. There is a need to understand the physicochemical factors that participate in DNA delivery protocols. Hence, this study provides new insights into the characterization of DNA/PEI complexes that will assist in more productive and reproducible TGE strategies. [ABSTRACT FROM AUTHOR]

Highlights • Responses of IgG, n-hHCP, histone, and DNA to pHs/conductivity were studied. • IgG loss was correlated with the precipitation of chromatin heteroaggregates. • Chromatin heteroaggregates were agglomerated along with the lowering pH. • Protein A chromatography was benefited from chromatin heteroaggregates reduction. Abstract Acid precipitation has been demonstrated as a clarification method for cell culture supernatant (CCS) pretreatment during Immunoglobulin G (IgG) purification. In this study, the responses of IgG, non-histone host cell protein (n-hHCP), histone, and DNA to different pHs in the presence of salt (NaCl) at various concentrations were systematically studied. IgG loss was closely associated with the precipitation of chromatin heteroaggregates, in which DNA/histone showed significant decreases along with the acidification of buffer environment. In addition, DNA showed full recovery after pH neutralization, while the low pH treatment induced histone precipitation was permanent and could not be reverted upon pH increase. Analytical size exclusion chromatography (SEC) profiles further indicated the agglomeration and reduction of chromatin heteroaggregates along with lower pH. Protein A chromatography benefited from the reduction of chromatin heteroaggregates and showed significant enhancement of the removal of impurities as well as for IgG recovery. For the first time, this study correlated CCS acidification with chromatin heteroaggregate removal and illustrated its ramification for the subsequent purification process. [ABSTRACT FROM AUTHOR]

Abstract Venoms of medically important scorpions from Buthidae family have been intensively studied, in contrast to non-buthid venoms, for which knowledge is scarce. In this work, we characterized the venom of a Diplocentridae species, Didymocentrus krausi , a small fossorial scorpion that inhabits the Tropical Dry Forest of Central America. D. krausi venom soluble fraction contains proteases with enzymatic activity on gelatin and casein. Mass spectrometry and venomic analysis confirmed the presence of elastase-like, cathepsin- O -like proteases and a neprilysin-like metalloproteinase. We did not detect phospholipase A 2 , C or D, nor hyaluronidase activity in the venom. By homology-based venom gland transcriptomic analysis, NDBPs, a β-KTx-like peptide, and other putative toxin transcripts were found, which, together with a p -benzoquinone compound present in the venom, could potentially explain its direct hemolytic and cytotoxic effects in several mammalian cell lines. Cytotoxicity of D. krausi venom was higher than the effect of venoms from two buthid scorpion species distributed in Costa Rica, Centruroides edwardsii and Tityus pachyurus. Even though D. krausi venom was not lethal to mice or crickets, when injected in mouse gastrocnemius muscle at high doses it induced pathological effects at 24 h, which include myonecrosis, weak hemorrhage, and inflammatory infiltration. We observed an apparent thrombotic effect in the skin blood vessels, but no in vitro fibrinogenolytic activity was detected. In crickets, D. krausi venom induced toxicity and paralysis in short periods of time. Graphical abstract Unlabelled Image Highlights • Didymocentrus krausi venom contains proteases and several types of peptides. • This venom is able to induce hemolysis and cytotoxicity, an effect produced by several components, including a p -benzoquinone. • In mice the venom is myonecrotic and induces weak hemorrhage and inflammation. • In insects this venom is toxic and induces paralysis. • No lethality was observed but in vitro this venom induces more toxicity than the venom of some buthids found in Costa Rica [ABSTRACT FROM AUTHOR]

Abstract The Nile tilapia Sox9b gene is characterized as a homolog of the mammalian Sox9 gene, which exhibits testis-biased expression and is involved in testis development. However, the transcriptional regulation of the Sox9b gene is poorly understood. In this study, we demonstrated that the male sex differentiation gene doublesex and mab-3 related transcription factor 1 (Dmrt1) was predominantly expressed in the Nile tilapia testis and that Dmrt1 knockdown in the Nile tilapia decreased the expression of the Sox9b gene in the testis. An in silico analysis predicted that the proximal promoter of the Nile tilapia Sox9b gene had two potential cis-regulatory elements (CREs) for the Dmrt1 transcription factor. Together, a luciferase reporter analysis and site-directed mutagenesis revealed that Dmrt1 increased the transcriptional activity of the Nile tilapia Sox9b promoter via a specific CRE near the translation start site. A chromatin immunoprecipitation (ChIP) analysis and an electrophoretic mobility shift assay (EMSA) confirmed that Dmrt1 could directly bind to this specific CRE for Dmrt1 in the Nile tilapia Sox9b promoter. Taken together, our results demonstrate that the male sex-differentiation factor Dmrt1 positively regulates the transcription of the Nile tilapia Sox9b gene by directly binding to a specific CRE within the Sox9b promoter. Highlights • Sox9b and Dmrt1 are predominately expressed in the Nile tilapia testis. • Dmrt1 knockdown in Nile tilapia decreases Sox9b transcription in testis. • Dmrt1 promotes the activity of the Nile tilapia Sox9b promoter via a specific CRE for Dmrt1. • Dmrt1 directly binds to a specific CRE within the Nile tilapia Sox9b promoter. [ABSTRACT FROM AUTHOR]

Highlights • The SMA copolymer was used to extract full-length human Kv channels, overexpressed in mammalian cells, in the absence of detergents. • This approach allowed to obtain water-soluble, monodisperse, concentrated SMALPs that contained human Kv channels suitable for structural studies. • Within SMALPs, the extracted channels retained their four-fold symmetry when studied by transmission electron microscopy (EM). Abstract Styrene-maleic acid (SMA) copolymers are used to extract lipid-encased membrane proteins from lipid bilayers in a detergent-free manner, yielding SMA lipid particles (SMALPs). SMALPs can serve as stable water-soluble nanocontainers for structural and functional studies of membrane proteins. Here, we used SMA copolymers to study full-length pore-forming α-subunits hKCNH5 and hKCNQ1 of human neuronal and cardiac voltage-gated potassium (Kv) channels, as well as the fusion construct comprising of an α-subunit hKCNQ1 and its regulatory transmembrane KCNE1 β-subunit (hKCNE1-hKCNQ1) with added affinity tags, expressed in mammalian COS-1 cells. All these recombinant proteins were shown to be functionally active. Treatment with the SMA copolymer, followed by purification on the affinity column, enabled extraction of all three channels. A DLS experiment demonstrated that negative stain electron microscopy and single particle image analysis revealed a four-fold symmetry within channel-containing SMALPs, which indicates that purified hKCNH5 and hKCNQ1 channels, as well as the hKCNE1-hKCNQ1 fusion construct, retained their structural integrity as tetramers. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • A fluoroquinoline derivate showed activity against L. infantum and L. amazonensis. • A low toxicity was found in mammalian cells. • The mechanism of action of this molecule was based on the parasite´s necrosis. • It was effective in the treatment of Leishmania -infected BALB/c mice. • The molecule can be considered as an antileishmanial candidate against human disease. Abstract New therapeutics against leishmaniasis are desirable, since the current drugs applied against this disease complex presents problems, such as the toxicity, high cost and/or parasite resistance. In the present study, a new fluoroquinoline derivate, namely 7-chloro-N-(4-fluorophenethyl)quinolin-4-amine or GF1061, was evaluated regarding to its in vitro antileishmanial action against Leishmania infantum and L. amazonensis species, as well as by its toxicity in mammalian cells and efficacy in the treatment of infected macrophages. The mechanism of action of this molecule in L. amazonensis and the therapeutic efficacy in infected BALB/c mice were also evaluated. Results showed that GF1061 was effective against both parasite species, showing selectivity index (SI) of 38.7 and 42.7 against L. infantum and L. amazonensis promastigotes, respectively, and of 45.0 and 48.9 against the amastigotes, respectively. Amphotericin B (AmpB), used as control, showed SI values of 6.6 and 8.8 against L. infantum and L. amazonensis promastigotes, respectively, and of 2.2 and 2.7 against the amastigotes, respectively. The molecule was effective in treat infected macrophages, as well as it induced alterations in the mitochondrial membrane potential, increase in the reactive oxygen species production, and in the cell integrity of the parasites. Regarding to the in vivo experiments, BALB/c mice (n = 8 per group) were subcutaneously infected with 106 L. amazonensis stationary promastigotes and, 60 days post-infection, they received saline or were treated during 10 days, once a day, with AmpB (1 mg/kg body weight) or GF1061 (5 mg/kg body weight). One day after the treatment, the infected tissue, spleen, liver, and draining lymph node (dLN) of the animals were collected, and the parasite load was evaluated. GF1061-treated mice, as compared to the saline and AmpB groups, showed significant reductions in the parasitism in the infected tissue (66% and 62%, respectively), liver (69% and 44%, respectively), spleen (71% and 38%, respectively), and dLN (72% and 48%, respectively). In conclusion, results suggested that GF1061 may be considered as a possible therapeutic target to be evaluated against leishmaniasis in other mammalian hosts. [ABSTRACT FROM AUTHOR]

Abstract Overflow metabolism is a common phenomenon observed at higher glycolytic flux in many bacteria, yeast (known as Crabtree effect), and mammalian cells including cancer cells (known as Warburg effect). This phenomenon has recently been characterized as the trade-offs between protein costs and enzyme efficiencies based on coarse-graining approaches. Moreover, it has been recognized that the glycolytic flux increases as the source of energy generation changes from energetically efficient respiration to inefficient respiro-fermentative or fermentative metabolism causing overflow metabolism. It is highly desired to clarify the metabolic regulation mechanisms behind such phenomena. Metabolic fluxes are located on top of the hierarchical regulation systems, and represent the outcome of the integrated response of all levels of cellular regulation systems. In the present article, we discuss about the different levels of regulation systems for the modulation of fluxes depending on the growth rate, growth condition such as oxygen limitation that alters the metabolism towards fermentation, and genetic perturbation affecting the source of energy generation from respiration to respiro-fermentative metabolism in relation to overflow metabolism. The intracellular metabolite of the upper glycolysis such as fructose 1,6-bisphosphate (FBP) plays an important role not only for flux sensing, but also for the regulation of the respiratory activity either directly or indirectly (via transcription factors) at higher growth rate. The glycolytic flux regulation is backed up (enhanced) by unphosphorylated EIIA and HPr of the phosphotransferase system (PTS) components, together with the sugar-phosphate stress regulation, where the transcriptional regulation is further modulated by post-transcriptional regulation via the degradation of mRNA (stability of mRNA) in Escherichia coli. Moreover, the channeling may also play some role in modulating the glycolytic cascade reactions. Highlights • Flux sensing metabolite such as FBP influences the respiratory activity • Source of energy generation affects the glycolytic flux and overflow metabolism • Sugar-phosphate stress, gene expression, and mRNA stability determine the flux [ABSTRACT FROM AUTHOR]

Abstract Protein arginine N -methyltransferase (PRMT) kinetic parameters have been catalogued over the past fifteen years for eight of the nine mammalian enzyme family members. Like the majority of methyltransferases, these enzymes employ the highly ubiquitous cofactor S -adenosyl- l -methionine as a co-substrate to methylate arginine residues in peptidic substrates with an approximately 4-μM median K M. The median values for PRMT turnover number (k cat) and catalytic efficiency (k cat /K M) are 0.0051 s−1 and 708 M−1 s−1, respectively. When comparing PRMT metrics to entries found in the BRENDA database, we find that while PRMTs exhibit high substrate affinity relative to other enzyme-substrate pairs, PRMTs display largely lower k cat and k cat /K M values. We observe that kinetic parameters for PRMTs and arginine demethylase activity from dual-functioning lysine demethylases are statistically similar, paralleling what the broader enzyme families in which they belong reveal, and adding to the evidence in support of arginine methylation reversibility. Graphical abstract Unlabelled Image Highlights • Comparisons of enzyme kinetic parameters from BRENDA database. • High substrate affinity and low turnover number and catalytic efficiency for PRMTs. • Substrate size and activity assay type related to PRMT K M. • Similar kinetic parameters for PRMTs and arginine demethylases. [ABSTRACT FROM AUTHOR]

Highlights • A cooperative metaheuristic method applied to the parameter estimation is proposed. • An improved sequential metaheuristic is run in parallel using multicores. • A new cooperative mechanism to exchange information is introduced. • The results present promising performance compared with other methods. Abstract Industrial bioprocesses development nowadays is concerned with producing chemicals using yeast, bacteria and therapeutic proteins in mammalian cells. This involves the utilization of microorganism cells as factories and re-engineering them in silico. The tools that could facilitate this process are known as the kinetic models. Kinetic models of cellular metabolism are important in assisting researchers to understand the rational design of biological systems, predicting metabolites production, and improving bio-products development. However, the most challenging task in model development is parameter estimation, which is the process of identifying an unknown value of model parameters which provides the best fit between the model output and a set of experimental data. Due to the increased complexity and high dimensionality of the models, which are extremely nonlinear and contain large numbers of kinetic parameters, parameter estimation is known to be difficult and time-consuming. This study proposes a cooperative enhanced scatter search with opposition-based learning schemes (CeSSOL) for parameter estimation in large-scale biology models. The method was executed in parallel with the proposed cooperative mechanism in order to exchange information (kinetic parameters) between individual threads. Each thread consists of different parameters settings that enhance the systemic properties in obtaining the global minimum. The performance of the proposed method was assessed against two large-scale microorganisms models using mammalian and bacteria cells. The results revealed that the proposed method recorded faster computation time compared to other methods. The study has also demonstrated that the proposed method can be used to provide more accurate and faster estimation of kinetic models, indicating the potential benefits of utilizing this method for expert systems of industrial biotechnology. [ABSTRACT FROM AUTHOR]

Outer membrane vesicles produced by Gram-negative bacteria have been studied for half a century but the possibility that Gram-positive bacteria secrete extracellular vesicles (EVs) was not pursued until recently due to the assumption that the thick peptidoglycan cell wall would prevent their release to the environment. However, following their discovery in fungi, which also have cell walls, EVs have now been described for a variety of Gram-positive bacteria. EVs purified from Gram-positive bacteria are implicated in virulence, toxin release, and transference to host cells, eliciting immune responses, and spread of antibiotic resistance. Listeria monocytogenes is a Gram-positive bacterium that causes listeriosis. Here we report that L. monocytogenes produces EVs with diameters ranging from 20 to 200 nm, containing the pore-forming toxin listeriolysin O (LLO) and phosphatidylinositol- specific phospholipase C (PI-PLC). Cell-free EV preparations were toxic to mammalian cells, the murine macrophage cell line J774.16, in a LLO-dependent manner, evidencing EV biological activity. The deletion of plcA increased EV toxicity, suggesting PI-PLC reduced LLO activity. Using simultaneous metabolite, protein, and lipid extraction (MPLEx) multiomics we characterized protein, lipid, and metabolite composition of bacterial cells and secreted EVs and found that EVs carry the majority of listerial virulence proteins. Using immunogold EM we detected LLO at several organelles within infected human epithelial cells and with high-resolution fluorescence imaging we show that dynamic lipid structures are released from L. monocytogenes during infection. Our findings demonstrate that L. monocytogenes uses EVs for toxin release and implicate these structures in mammalian cytotoxicity. [ABSTRACT FROM AUTHOR]

Abstract CXCL14 is a CXC chemokine family that exhibits antimicrobial activity and contains an amphipathic cationic α-helical region in the C-terminus, a characteristic structure of antimicrobial peptides (AMPs). In this study, we designed three analogs of CXCL14 59–75 (named CXCL14-C17) corresponding to the C-terminal α-helix of CXCL14, which displayed potential antimicrobial activity against a wide variety of gram-negative and gram-positive bacteria with minimum inhibitory concentrations of 4−16 μM without mammalian cell toxicity. Furthermore, two CXCL14-C17 analogs (CXCL14-C17-a1 and CXCL14-C17-a3) with improved cell selectivity were engineered by introducing Lys, Arg, or Trp in CXCL14-C17. Additionally, CXCL14-C17 analogs showed much greater synergistic effect (FICI: 0.3125–0.375) with chloramphenicol and ciprofloxacin against multidrug-resistant Pseudomonas aeruginosa (MDRPA) than LL-37 did (FICI: 0.75–1.125). CXCL14-C17 analogs were more active against antibiotic-resistant bacteria including methicillin-resistant Staphylococcus aureus (MRSA), MDRPA, and vancomycin-resistant Enterococcus faecium (VREF) than LL-37 and melittin. In particular, CXCL14-C17-a2 and CXCL14-C17-a3 completely inhibited the biofilm formation at sub-MIC and all of the peptides were able to eliminate pre-formed biofilm as well. Membrane depolarization, flow cytometry, sytox green uptake, ONPG hydrolysis and confocal microscopy revealed the possible target of the native peptide (CXCL14-C17) to likely be intracellular, and the amphipathic designed analogs targeted the bacterial membrane. CXCL14-C17 also showed DNA binding characteristic activity similar to buforin-2. Interestingly, CXCL14-C17-a2 and CXCL14-C17-a3 effectively inhibited the production and expression of nitric oxide (NO), tumor necrosis factor (TNF)-α, interleukin (IL)-6, and monocyte chemoattractant protein (MCP)-1 from lipopolysaccharide (LPS)-stimulated RAW264.7 cells, suggesting that these peptides could be promising anti-inflammatory and antimicrobial agents. Graphical abstract Unlabelled Image Highlights • CXCL14-C17 corresponding to the C-terminal α-helix of a CXC chemokine family CXCL14 and its analogs were designed and synthesized. • CXCL14-C17 displayed potent antimicrobial activity (MIC range: 4−16μM) without mammalian cell toxicity. • The main target of CXCL14-C17 and its analogs is intracellular and bacterial membrane, respectively. • CXCL14-C17 analogs were more active against antibiotic-resistant bacteria including MRSA, MDRPA and VREF than LL-37 and melittin. • CXCL14-C17-a2 and CXCL14-C17-a3 could be promising antimicrobial and anti-inflammatory agents. [ABSTRACT FROM AUTHOR]

Abstract Chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC-MS) has a potential to become a very powerful platform for comprehensive and quantitative analysis of metabolites in cellular metabolomics. While CIL LC-MS with rationally designed reagents for labeling can provide much enhanced detection and quantification of metabolites, pre-analytical process such as cell harvest and cell lysis is also a critical step in the overall workflow for metabolomic analysis. In this study, we examined various combinations of cell harvest and cell lysis methods in order to develop a simple and efficient method for harvesting and lysing adherent mammalian cells tailored to CIL LC-MS-based cellular metabolomics. We evaluated and compared two cell harvest methods (physical scraping and trypsinization) and two cell lysis methods (glass-bead-assisted lysis and freeze-thaw-cycle lysis). We used two types of commonly used mammalian cells, HeLa and MCF-7 cells, to cross-validate the findings. LC-UV quantification of the labeled metabolites after dansylation of cell extracts was used to compare the overall cell harvest and cell lysis efficiencies among different combination methods. It was found that scraping combined with freeze-thaw-cycle lysis gave the highest total metabolite concentration. We also performed multivariate and univariate analyses of the amine/phenol submetabolome data generated from different preparations to investigate the impact of cell harvest and lysis methods on cellular metabolome profiles. Comparing to scraping, trypsinization caused more significant metabolome changes likely due to metabolite leakage and metabolite level changes. The cellular metabolomes obtained from the two lysis methods were found to be similar; however, freeze-thaw-cycle lysis gave a higher lysis efficacy, compared to the glass bead method. We concluded that the combination of scraping and freeze-thaw-cycle was optimal for harvesting and lysing adherent mammalian cells for CIL LC-MS metabolomics. Graphical abstract Image 1 Highlights • A method was developed for simple and efficient cell harvest and lysis for cellular metabolomics. • Dansylation isotope labeling LC-MS was used for profiling the amine/phenol submetabolomes of cell extracts. • Scraping and trypsinization methods were compared for harvesting adherent cells. • Freeze-thaw-cycle and glass-bead-assisted methods were compared for cell lysis. • The combination of scraping and freeze-thaw-cycle methods was found to be optimal for handling adherent cells. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • An iterative SAR was carried out on the antifungal peptoid AEC5. • Subtle modifications improved both antifungal potency and selectivity. • β-5 shows promise to contribute to the challenging field of antifungals. Abstract As proteolytically stable peptidomimetics, peptoids could serve as antifungal agents to supplement a therapeutic field wrought with toxicity issues. We report the improvement of an antifungal peptoid, AEC5, through an iterative structure-activity relationship study. A sarcosine scan was used to first identify the most pharmacophorically important peptoid building blocks of AEC5, followed by sequential optimization of each building block. The optimized antifungal peptoid from this study, β-5, has improved potency towards Cryptococcus neoformans and decreased toxicity towards mammalian cells. For example, the selectivity ratio for C. neoformans over mammalian fibroblasts was improved from 8 for AEC5 to 37 for β-5. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Methodologies for unravelling the control of mRNA translation in CHO cells. • Long non-coding RNA targets for CHO cell engineering. • Description of how codon bias impacts on fidelity and efficiency of translation. • Engineering of codon bias and tRNAs. Chinese hamster ovary cells are the main mammalian cell expression system currently used for the production of recombinant protein biopharmaceuticals. One of the key processes determining the achievable biomass of cells in the bioreactor and the yield and quality of recombinant protein from such systems is mRNA translation. Translation is the process by which ribosomes and associated cellular machinery decode an mRNA to produce a polypeptide. In recent years the roles of different classes of non-coding RNAs in controlling global and transcript specific mRNA translation has also come to light. Here we review approaches to engineer the translational machinery and non-coding RNAs, particularly long non-coding RNAs and tRNAs in CHO cells and then outline the challenges and potential of such approaches to revolutionize the yields and quality of recombinant protein from CHO and other mammalian cell expression systems. [ABSTRACT FROM AUTHOR]

Chinese hamster ovary (CHO) cells are the most prevalent mammalian cell factories for producing therapeutic biologics, due to its capacity for complex post-translational modifications, ability to grow well in suspension cultures and low susceptibility to human viral infections. Significant advances in various modules of the CHO cell line development and engineering (CLD&E) have contributed to up to 100-fold increase in the product yields over the last three decades. Although production yield still remains the major focus in CLD&E, product quality and long-term stability have increasingly appeared to be the additional criteria. Towards achieving such goals, various platforms involving high-throughput clonal evaluation in automated manner, efficient vector designs, RNA interference methods and genome editing techniques have been developed to generate highly productive clones much faster with desired quality attributes and cell line traits. Since CHO genome was sequenced, we can now systematically characterize CHO cells using high-throughput omics profiles and in silico computational models, thereby identifying relevant targets for rational cell engineering which can be readily validated by the emerging genome editing techniques in a targeted and precise manner. In this review, we summarize the history of CHO CLD&E, and then describe the major technological advancements along with the application areas. Lastly, our perspectives on the next generation CLD&E are provided within the context of mammalian systems biotechnology. [ABSTRACT FROM AUTHOR]

Hydrolysates play important roles in enhancing the productivity of recombinant proteins in mammalian cell cultures. Lacking of detailed understanding of the mechanisms, hydrolysate is commonly regarded as an unstable factor which should be used with cautions. A yeast extract (YE) was approved to improve the Fc-fusion protein productivity in a recombinant Chinese hamster ovary (CHO) cell line. To elucidate the responses of cells to hydrolysates, we further elaborate their physiological changes during the processes in the presence and absence of YE. Firstly, cell sizes and the cellular components including dry cell weight, cellular fatty acid, and total cellular protein were increased in the presence of YE. Then, by comparing the extracellular and intracellular concentrations of the main metabolites and their consumption rates, we excluded the possibility of nutrient depletion in the absence of YE and observed a distinct improvement on the net consumption rates of metabolites in the presence of YE. Furthermore, the increase on the contents of intracellular nucleotides illustrated an abundance of the nucleic acid precursors and energy charge for recombinant protein synthesis in the presence of YE. In conclusion, this study systematically elucidated YE enhanced cell mass and capacity, activated substrate and energy metabolism of cells in addition to a boost in product synthesis process. The findings provide valuable information for process optimization and cell engineering. Highlights • Yeast extract enhanced the assimilation processes of CHO cells for most nutrients. • Purine nucleotide contents at protein production stage were increased by yeast extract. • Higher energy charges at protein production stage were achieved with yeast extract. [ABSTRACT FROM AUTHOR]

Graphical abstract Abstract Lamin A contributes to the structure of nuclei in all mammalian cells and plays an important role in cell division and migration. Mature lamin A is derived from a farnesylated precursor protein, known as prelamin A, which undergoes post-translational cleavage catalyzed by the zinc metalloprotease STE24 (ZPMSTE24). Accumulation of farnesylated prelamin A in the nuclear envelope compromises cell division, impairs mitosis and induces an increased expression of inflammatory gene products. ZMPSTE24 has been proposed as a potential therapeutic target in oncology. A library of peptidomimetic compounds were synthesized and screened for their ability to induce accumulation of prelamin A in cancer cells and block cell migration in pancreatic ductal adenocarcinoma cells. The results of this study suggest that inhibitors of lamin A maturation may interfere with cell migration, the biological process required for cancer metastasis. [ABSTRACT FROM AUTHOR]

Highlights • Ribosome footprint profiling (RiboSeq) has illuminated translation in exquisite detail. • A range of RiboSeq derived methods is available to study ribosomal elongation and initiation. • RiboSeq is poised to enable enhanced translation control in mammalian cell factories for biopharmaceutical production. Biopharmaceuticals such as monoclonal antibodies have revolutionised the treatment of a variety of diseases. The production of recombinant therapeutic proteins, however, remains expensive due to the manufacturing complexity of mammalian expression systems and the regulatory burden associated with administrating these medicines to patients in a safe and efficacious manner. In recent years, academic and industrial groups have begun to develop a greater understanding of the biology of host cell lines, such as Chinese hamster ovary (CHO) cells and utilise that information for process development and cell line engineering. In this review, we focus on ribosome footprint profiling (RiboSeq), an exciting next generation sequencing (NGS) method that provides genome-wide information on translation, and discuss how its application can transform our understanding of therapeutic protein production. [ABSTRACT FROM AUTHOR]

Abstract Information about the distributions of cholesterol and sphingolipids within the plasma membranes of mammalian cells provides insight into the roles of these molecules in membrane function. In this report, high-resolution secondary ion mass spectrometry was used to image the distributions of metabolically incorporated rare isotope-labeled sphingolipids and cholesterol on the surfaces of nonpolarized epithelial cells. Sphingolipid domains that were not enriched with cholesterol were detected in the plasma membranes of subconfluent Madin-Darby canine kidney cells. Surprisingly, cholesterol-enriched sphingolipid patches were observed on the substrate adjacent to these cells. Based on the shapes of these cholesterol-enriched sphingolipid patches on the substrate and their proximity to cellular projections, we hypothesize that they are deposits of membranous particles released by the cell. Highlights • Plasma membranes of nonpolarized MDCK cells contain sphingolipid domains. • Uniform cholesterol distribution in the plasma membranes of nonpolarized MDCK cells • Cholesterol-rich sphingolipid patches detected on the substrate next to MDCK cells • No cholesterol-sphingolipid domains in the plasma membranes of nonpolarized MDCK cells [ABSTRACT FROM AUTHOR]

Graphical abstract Abstract (+)-Epogymnolactam (1) was discovered as a novel autophagy inducer from a culture of Gymnopus sp. in our laboratory. To determine structure-activity relationships among (+)-epogymnolactam analogues comparing with cerulenin (2), we synthesized 5 analogues including (−)-epogymnolactam (3) having each different functional group, and 3 analogues with different side-chain lengths. Five analogues, 3 , 4 , 5 , 6 , and 7 did not significantly increase the ratio of LC3-II to LC3-I as an autophagy marker in NIH3T3 cells. These results suggest that presence and stereochemistry of (2 R ,3 S)-epoxy group and cyclic syn -form (1b) of 1 are important for the activity as autophagy inducer. Hexyl analogue (8) as well as 1 having butyl side-chain dose-dependently increased the ratio of LC3-II to LC3-I, whereas octyl analogue (9) and 2 rather decreased the ratio. Decyl analogue (10) did not give a change in the ratio. Although 8 seemed to be an excellent autophagy inducer, it dose-dependently increased SQSTM1 (p62) as in the case of 2 , whereas 1 showed a slight dose-dependent decrease of p62 as an index of autophagic protein degradation. These observations suggest that 8 is an autophagy modulator with different molecular target from 1 or 2. [ABSTRACT FROM AUTHOR]

T-2 toxin is the most toxic member of trichothecene mycotoxin. So far, the mechanism of mitochondrial toxicity and protective mechanism in mammalian cells against T-2 toxin are not fully understood. In this study, we aimed to investigate the cellular and mitochondrial toxicity of T-2 toxin, and the cellular protective mechanisms in rat pituitary GH3 cells. We showed that T-2 toxin significantly increased reactive oxygen species (ROS) and DNA damage and caused apoptosis in GH3 cells. T-2 toxin induced abnormal cell morphology, cytoplasm and nuclear shrinkage, nuclear fragmentation and formation of apoptotic bodies and autophagosomes. The mitochondrial degradative morphologies included local or total cristae collapse and small condensed mitochondria. T-2 toxin decreased the mitochondrial membrane potential. However, T-2 toxin significantly increased the superoxide dismutase (SOD) activity and expression of antioxidant genes glutathione peroxidase 1 (GPx-1), catalase (CAT), mitochondria-specific SOD-2 and mitochondrial uncoupling protein-1, -2 and -3 (UCP-1, 2 and 3). Interestingly, T-2 toxin increased adenosine triphosphate (ATP) levels and mitochondrial complex I activity, and increased the expression of most of mitochondrial electron transport chain subunits tested and critical transcription factors controlling mitochondrial biogenesis and mitochondrial DNA transcription and replication. T-2 toxin increased mitophagic activity by increasing the expression of mitophagy-specific proteins NIP-like protein X (NIX), PTEN-induced putative kinase protein 1 (PINK1) and E3 ubiquitin ligase Parkin. T-2 toxin activated the protective protein kinase A (PKA) signaling pathway, which activated the nuclear factor (erythroid-derived 2)-like 2 (Nrf2)/PINK1/Parkin pathway to mediate mitophagy. Taken together, our results suggested that the mammalian cells could increase their resistance against T-2 toxin by increasing the antioxidant activity, mitophagy and mitochondrial function. [ABSTRACT FROM AUTHOR]

Abstract Effective transgene expression in mammalian cells relies on successful delivery, cytoplasmic trafficking, and nuclear translocation of the delivered vector, but delivery is impeded by several formidable physicochemical barriers on the surface of and within the target cell. Although methods to overcome cellular exclusion and endosomal entrapment have been studied extensively, strategies to overcome inefficient nuclear entry and subsequent intranuclear barriers to effective transient gene expression have only been sparsely explored. In particular, the role of nuclear packaging of DNA with histone proteins, which governs endogenous gene expression, has not been extensively elucidated in the case of exogenously delivered plasmids. In this work, a parallel screen of small molecule inhibitors of chromatin-modifying enzymes resulted in the identification of class I/II HDACs, sirtuins, LSD1, HATs, and the methyltransferases EZH2 and MLL as targets whose inhibition led to the enhancement of transgene expression following polymer-mediated delivery of plasmid DNA. Quantitative PCR studies revealed that HDAC inhibition enhances the amount of plasmid DNA delivered to the nucleus in UMUC3 human bladder cancer cells. Native chromatin immunoprecipitation (N-ChIP)-qPCR experiments in CHO-K1 cells indicated that plasmids indeed interact with intracellular core Histone H3, and inhibitors of HDAC and LSD1 proteins are able to modulate this interaction. Pair-wise treatments of effective inhibitors led to synergistic enhancement of transgene expression to varying extents in both cell types. Our results demonstrate that the ability to modulate enzymes that play a role in epigenetic processes can enhance the efficacy of non-viral gene delivery, resulting in significant implications for gene therapy and industrial biotechnology. Graphical abstract Unlabelled Image Highlights • Inhibition of chromatin-modifying enzymes enhances transgene expression. • Combinatorial enzyme inhibition further affects transient expression. • HDAC inhibition increases nuclear entry of plasmid in UMUC3 bladder cancer cells. • Exogenous plasmids interact with endogenous core histone H3. • Inhibition of HDAC and/or LSD1 modulates plasmid/histone H3 interactions. [ABSTRACT FROM AUTHOR]

Analysis of metabolites is often performed using separations coupled to mass spectrometry which is challenging due to their vast structural heterogeneity and variable charge states. Metabolites are often separated based on their class/functional group which in large part determine their acidity or basicity. This charge state dictates the ionization mode and efficiency of the molecule. To improve the sensitivity and expand the coverage of the mammalian metabolome, multifunctional derivatization with sheathless CE-ESI-MS was undertaken. In this work, amines, hydroxyls and carboxylates were labeled with tertiary amines tags. This derivatization was performed in under 100 min and resulted in high positive charge states for all analytes investigated. Amino acids and organic acids showed average limits of detection of 76 nM with good linearity of 0.96 and 10% RSD for peak area. Applying this metabolomic profiling system to bovine aortic endothelial cells showed changes in 15 metabolites after treatment with high glucose. The sample injection volume on-capillary was <300 cells for quantitative analyses. Targeted metabolites were found in human tissue, which indicates possible application of the system complex metabolome quantitation. [ABSTRACT FROM AUTHOR]

In-situ Raman spectroscopy is frequently applied to monitor and even control the glucose concentration of monoclonal antibody producing mammalian cell cultivations. Previous studies used the PLSR algorithm only, however other multivariate algorithms were applied successfully for different protein production processes. In this study, four mammalian cell cultivation runs were followed with Raman spectroscopy and the spectra were analysed quantitatively and qualitatively as well. The PCA analysis showed that one of the most dominant factors in the Raman spectra were the concentration of glucose, which strongly correlated with the score values of the eighth principal component. This observation further substantiated that Raman spectroscopy is an excellent tool for bioprocess monitoring and induced the test of the Multivariate Linear Regression (MLR), Principal Component Regression (PCR) and Partial Least Squares Regression (PLSR) algorithms, using the results of the PCA as one of the variable selection techniques, to determine the glucose concentration during cultivation. However, the novel variable selection technique of PCA correlation enhanced only the model accuracy when it was applied with MLR and only model robustness was increased when it was used with PCR and PLSR because the relatively strong Raman signal of glucose concentration seemed to be enough to build an accurate model on. Therefore, PLSR, the most advanced algorithm of the three, delivered the lowest 2.21 mM RMSEP but it was demonstrated that in certain cases PCR could also produce satisfactorily results. [ABSTRACT FROM AUTHOR]

Biofilms present a major problem to industry and healthcare worldwide. Composed of a population of surface-attached microbial cells surrounded by a protective extracellular polysaccharide matrix, they are responsible for increased tolerance to antibiotics, treatment failure and a resulting rise in antimicrobial resistance. Here we demonstrate that self-assembled peptide nanostructures composed of a diphenylalanine motif provide sufficient antibacterial activity to eradicate mature biofilm forms of bacteria widely implicated in hospital infections. Modification of terminal functional groups to amino (–NH 2 ), carboxylic acid (–COOH) or both modalities, and switch to d-isomers, resulted in changes in antibacterial selectivity and mammalian cell toxicity profiles. Of the three peptide nanotubes structures studied (NH 2 -FF-COOH, NH 2 -ff-COOH and NH 2 -FF-NH 2 ), NH 2 -FF-COOH demonstrated the most potent activity against both planktonic (liquid, free-floating) and biofilm forms of bacteria, possessing minimal mammalian cell toxicity. NH 2 -FF-COOH resulted in greater than 3 Log 10 CFU/mL viable biofilm reduction (>99.9%) at 5 mg/mL and total biofilm kill at 10 mg/mL against Staphylococcus aureus after 24 h exposure. Scanning electron microscopy proved that antibiofilm activity was primarily due to the formation of ion channels and/or surfactant-like action, with NH 2 -FF-COOH and NH 2 -ff-COOH capable of degrading the biofilm matrix and disrupting cell membranes, leading to cell death in Gram-positive bacterial isolates. Peptide-based nanotubes are an exciting platform for drug delivery and engineering applications. This is the first report of using peptide nanotubes to eradicate bacterial biofilms and provides evidence of a new platform that may alleviate their negative impact throughout society. Statement of Significance We outline, for the first time, the antibiofilm activity of diphenylalanine (FF) peptide nanotubes. Biofilm bacteria exhibit high tolerance to antimicrobials 10–10,000 times that of free-flowing planktonic forms. Biofilm infections are difficult to treat using conventional antimicrobial agents, leading to a rise in antimicrobial resistance. We discovered nanotubes composed of NH 2 -FF-COOH demonstrated potent activity against staphylococcal biofilms implicated in hospital infections, resulting in complete kill at concentrations of 10 mg/mL. Carboxylic acid terminated FF nanotubes were able to destroy the exopolysaccharide architecture of staphylococcal biofilms expressing minimal toxicity, highlighting their potential for use in patients. Amidated (NH 2 -FF-NH 2 ) forms demonstrated reduced antibiofilm efficacy and significant toxicity. These results contribute significantly to the development of innovative antibacterial technologies and peptide nanomaterials. [ABSTRACT FROM AUTHOR]

Proteins in mammalian cells exhibit optimal stability at physiological temperatures, and even small temperature variations may cause unfolding and nonspecific aggregation. Because this process leads to a loss of function of the affected polypeptides and to cytotoxic stress, formation of protein aggregates has been recognized as a major pathogenic factor in human diseases. In this study, we determined the impact of physiological heat stress on mitochondria isolated from HeLa cells. We found that the heat-stressed mitochondria had lower membrane potential and ATP level and exhibited a decreased production of reactive oxygen species. An analysis of the mitochondrial proteome by 2D PAGE showed that the overall solubility of endogenous proteins was only marginally affected by elevated temperatures. However, a small subset of polypeptides exhibited an high sensitivity to heat stress. The mitochondrial translation elongation factor Tu (Tufm), a protein essential for organellar protein biosynthesis, was highly aggregation-prone and lost its solubility already under mild heat-stress conditions. Moreover, mitochondrial translation and the import of cytosolic proteins were defective in the heat-stressed mitochondria. Both types of nascent polypeptides, produced by translation or imported into the mitochondria, exhibited a strong tendency to aggregate in the heat-exposed mitochondria. We propose that a fast and specific inactivation of elongation factors may prevent the accumulation of misfolded nascent polypeptides and may thereby attenuate proteotoxicity under heat stress. [ABSTRACT FROM AUTHOR]

Using a classical hybridization approach, a series of 1 H -benzo[ d ]imidazoles and 3,4-dihydroquinazolin-4-ones were synthesized (39 examples) and evaluated as inhibitors of Mycobacterium tuberculosis growth. Chemical modification studies yielded potent antitubercular agents with minimum inhibitory concentration (MIC) values as low as 0.24 μM against M. tuberculosis H37Rv strain. Further, the synthesized compounds were active against four drug-resistant strains containing different levels of resistance for the first line drugs. These molecules were devoid of apparent toxicity to HepG2, HaCat, and Vero cells with IC 50s  > 30 μM. Viability in mammalian cell cultures was evaluated using MTT and neutral red assays. In addition, some 3,4-dihydroquinazolin-4-ones showed low risk of cardiac toxicity, no signals of neurotoxicity or morphological alteration in zebrafish ( Danio rerio ) toxicity models. 3,4-Dihydroquinazolin-4-ones 9q and 9w were considered the lead compounds of these series of molecules with MIC values of 0.24 μM and 0.94 μM against M. tuberculosis H37Rv, respectively. Taken together, these data indicate that this class of compounds may furnish candidates for future development of novel anti-TB drugs. [ABSTRACT FROM AUTHOR]

The Hippo pathway plays an important role in regulating tissue homeostasis, and its effectors, the transcriptional co-activators Yes-associated protein (YAP) and WW domain-containing transcription regulator 1 (WWTR1 or TAZ), are responsible for mediating the vast majority of its physiological functions. Although YAP and TAZ are thought to be largely redundant and similarly regulated by Hippo signaling, they have developmental, structural, and physiological differences that suggest they may differ in their regulation and downstream functions. To better understand the functions of YAP and TAZ in the Hippo pathway, using CRISPR/Cas9, we generated YAP KO, TAZ KO, and YAP/TAZ KO cell lines in HEK293A cells. We evaluated them in response to many environmental conditions and stimuli and used RNA-Seq to compare their transcriptional profiles. We found that YAP inactivation has a greater effect on cellular physiology (namely, cell spreading, volume, granularity, glucose uptake, proliferation, and migration) than TAZ inactivation. However, functional redundancy between YAP and TAZ was also observed. In summary, our findings confirm that the Hippo pathway effectors YAP and TAZ are master regulators for multiple cellular processes but also reveal that YAP has a stronger influence than TAZ. [ABSTRACT FROM AUTHOR]

In the yeast Saccharomyces cerevisiae, genomic instability in rDNA repeat sequences is an underlying cause of cell aging and is suppressed by the chromatin-silencing factor Sir2. In humans, rDNA instability is observed in cancers and premature aging syndromes, but its underlying mechanisms and functional consequences remain unclear. Here, we uncovered a pivotal role of sirtuin 7 (SIRT7), a mammalian Sir2 homolog, in guarding against rDNA instability and show that this function of SIRT7 protects against senescence in primary human cells. We found that, mechanistically, SIRT7 is required for association of SNF2H (also called SMARCA5, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin, subfamily A, member 5), a component of the nucleolar heterochromatin-silencing complex NoRC, with rDNA sequences. Defective rDNA-heterochromatin silencing in SIRT7-deficient cells unleashed rDNA instability, with excision and loss of rDNA gene copies, which in turn induced acute senescence. Mounting evidence indicates that accumulation of senescent cells significantly contributes to tissue dysfunction in aging-related pathologies. Our findings identify rDNA instability as a driver of mammalian cellular senescence and implicate SIRT7-dependent heterochromatin silencing in protecting against this process. [ABSTRACT FROM AUTHOR]

The cholinergic α7 nicotinic receptor gene, CHRNA7, encodes a subunit that forms the homopentameric α7 receptor, involved in learning and memory. In humans, exons 5-10 in CHRNA7 are duplicated and fused to the FAM7A genetic element, giving rise to the hybrid gene CHRFAM7A. Its product, dupα7, is a truncated subunit lacking part of the N-terminal extracellular ligand-binding domain and is associated with neurological disorders, including schizophrenia, and immunomodulation. We combined dupα7 expression on mammalian cells with patch clamp recordings to understand its functional role. Transfected cells expressed dupα7 protein, but they exhibited neither surface binding of the α7 antagonist α-bungarotoxin nor responses to acetylcholine (ACh) or to an allosteric agonist that binds to the conserved transmembrane region. To determine whether dupα7 assembles with α7, we generated receptors comprising α7 and dupα7 subunits, one of which was tagged with conductance substitutions that report subunit stoichiometry and monitored ACh-elicited channel openings in the presence of a positive allostericα7 modulator.Wefound thatα7 and dupα7 subunits co-assemble into functional heteromeric receptors, which require at least two α7 subunits for channel opening, and that dupα7's presence in the pentameric arrangement does not affect the duration of the potentiated events compared with that of α7. Using an α7 subunit mutant, we found that activation of (α7)2(dupα7)3 receptors occurs through ACh binding at theα7/α7 interfacial binding site. Our study contributes to the understanding of the modulation of α7 function by the human specific, duplicated subunit, associated with human disorders. [ABSTRACT FROM AUTHOR]

Turnip yellow mosaic virus (TYMV) was able to enter animal cells when the spherical plant virus was conjugated with Tat, a cell penetrating peptide (CPP). Tat was chemically attached to the surface lysine residues of TYMV using hydrazone chemistry. Baby hamster kidney (BHK) cells were incubated with either unmodified or Tat-conjugated TYMV and examined by flow cytometry and confocal microscopic analyses. Tat conjugation was shown to be more efficient than Lipofectamine in allowing TYMV to enter the mammalian cells. Tat-assisted-transfection was also associated with less loss of cell viability than lipofection. Among the CPPs tested (Tat, R8, Pep-1 and Pen), it was observed that R8 and Pen were also effective while Pep-1 was not. We also examined if the internal space of TYMV can be used to load fluorescein dye as a model cargo. When TYMV is treated by freezing and thawing, the virus is known to convert into a structure with a 6–8 nm hole and release viral RNA. When the resultant pot-like particles were reacted with fluorescein-5-maleimide using interior sulfhydryl groups as conjugation sites, about 145 fluorescein molecules were added per particle. The fluorescein-loaded TYMV particles were conjugated with Tat and introduced into BHK cells, again with higher transfection efficiency compared to lipofection. Our studies demonstrate the potential of modified TYMV as an efficient system for therapeutic cargo delivery to mammalian cells. [ABSTRACT FROM AUTHOR]

In mammalian cells, autophagy plays crucial roles in restricting further spread of invading bacterial pathogens. Previous studies have established that the Salmonella virulence factors SseF and SseG are required for intracellular bacterial survival and replication. However, the underlying mechanism by which these two effectors facilitate bacterial infection remains elusive. Here, we report that SseF and SseG secreted by Salmonella Typhimurium (S. Typhimurium) inhibit autophagy in host cells and thereby establish a replicative niche for the bacteria in the cytosol. Mechanistically, SseF and SseG impaired autophagy initiation by directly interacting with the small GTPase Rab1A in the host cell. This interaction abolished Rab1A activation by disrupting the interaction with its guanine nucleotide exchange factor (GEF), the TRAPPIII (transport protein particle III) complex. This disruption of Rab1A signaling blocked the recruitment and activation of Unc-51--like autophagy-activating kinase 1 (ULK1) and decreased phosphatidylinositol 3-phosphate biogenesis, which ultimately impeded autophagosome formation. Furthermore, SseF- or SseG-deficient bacterial strains exhibited reduced survival and growth in both mammalian cell lines and mouse infection models, and Rab1A depletion could rescue these defects. These results reveal that virulence factor--dependent inactivation of the small GTPase Rab1A represents a previously unrecognized strategy of S. Typhimurium to evade autophagy and the host defense system. [ABSTRACT FROM AUTHOR]

The vacuolar H+-ATPase (V-ATPase) is an ATP-driven proton pump involved in many cellular processes. An important mechanism by which V-ATPase activity is controlled is the reversible assembly of its two domains, namely the peripheral V1 domain and the integral V0 domain. Although reversible assembly is conserved across all eukaryotic organisms, the signaling pathways controlling it have not been fully characterized. Here, we identify glucose starvation as a novel regulator of V-ATPase assembly in mammalian cells. During acute glucose starvation, the V-ATPase undergoes a rapid and reversible increase in assembly and activity as measured by lysosomal acidification. Because the V-ATPase has recently been implicated in the activation of AMP kinase (AMPK), a critical cellular energy sensor that is also activated upon glucose starvation, we compared the time course of AMPK activation and V-ATPase assembly upon glucose starvation. We observe that AMPK activation precedes increased V-ATPase activity. Moreover, the starvation-induced increase in V-ATPase activity and assembly are prevented by the AMPK inhibitor dorsomorphin. These results suggest that increased assembly and activity of the V-ATPase upon glucose starvation are dependent upon AMPK. We also find that the PI3K/Akt pathway, which has previously been implicated in controlling V-ATPase assembly in mammalian cells, also plays a role in the starvation-induced increase in V-ATPase assembly and activity. These studies thus identify a novel stimulus of V-ATPase assembly and a novel signaling pathway involved in regulating this process. The possible function of starvation-induced increase in lysosomal V-ATPase activity is discussed. [ABSTRACT FROM AUTHOR]

Dengue has emerged as a major mosquito-borne disease in the tropics and subtropics. In severe dengue, enhanced microvascular endothelial permeability leads to plasma leakage. Direct dengue virus (DENV) infection in human microvascular endothelial cells (HMEC-1) can enhance trans-endothelial leakage. Using a microarray-based analysis, we identified modulation of key endothelial cell signaling pathways in DENV-infected HMEC-1 cells. One among them was the sphingolipid pathway that regulates vascular barrier function. Sphingosine-1-phosphate receptor 2 (S1PR2) and S1PR5 showed significant up-regulation in the microarray data. In DENV-infected cells, the kinetics of S1PR2 transcript expression and enhanced in vitro trans-endothelial permeability showed a correlation. We also observed an internalization and cytoplasmic translocation of VE-Cadherin, a component of adherens junctions (AJ), upon infection indicating AJ disassembly. Further, inhibition of S1PR2 signaling by a specific pharmacological inhibitor prevented translocation of VE-Cadherin, thus helping AJ maintenance, and abrogated DENV-induced trans-endothelial leakage. Our results show that sphingolipid signaling, especially that involving S1PR2, plays a critical role in vascular leakage in dengue. [ABSTRACT FROM AUTHOR]

Mammalian cell entry protein (Mce4A) is a member of MCE-family, and is being considered as a potential drug target of Mycobacterium tuberculosis infection because it is required for invasion and latent survival of pathogen by utilizing host's cholesterol. In the present study, we performed molecular docking followed by 100 ns MD simulation studies to understand the mechanism of interaction of Mce4A to the cholesterol derivatives and probucol. The selected ligands, cholesterol, 25-hydroxycholesterol, 5-cholesten-3β-ol-7-one and probucol bind to the predicted active site cavity of Mce4A, and complexes remain stable during entire simulation of 100 ns. In silico studies were further validated by fluorescence-binding studies to calculate actual binding affinity and number of binding site(s). The non-toxicity of all ligands was confirmed on human monocytic cell (THP1) by MTT assay. This work provides a deeper insight into the mechanism of interaction of Mce4A to cholesterol derivatives, which may be further exploited to design potential and specific inhibitors to ameliorate the Mycobacterium pathogenesis. [ABSTRACT FROM AUTHOR]

One of the greatest challenges for mass spectrometry (MS)-based proteomics is the limited ability to analyze small samples. Here we investigate the relative contributions of liquid chromatography (LC), MS instrumentation and data analysis methods with the aim of improving proteome coverage for sample sizes ranging from 0.5 ng to 50 ng. We show that the LC separations utilizing 30-μm- i.d. columns increase signal intensity by >3-fold relative to those using 75-μm- i.d. columns, leading to 32% increase in peptide identifications. The Orbitrap Fusion Lumos MS significantly boosted both sensitivity and sequencing speed relative to earlier generation Orbitraps (e.g., LTQ-Orbitrap), leading to a ∼3-fold increase in peptide identifications and 1.7-fold increase in identified protein groups for 2 ng tryptic digests of the bacterium S. oneidensis . The Match Between Runs algorithm of open-source MaxQuant software further increased proteome coverage by ∼95% for 0.5 ng samples and by ∼42% for 2 ng samples. Using the best combination of the above variables, we were able to identify >3000 proteins from 10 ng tryptic digests from both HeLa and THP-1 mammalian cell lines. We also identified >950 proteins from subnanogram archaeal/bacterial cocultures. The present ultrasensitive LC–MS platform achieves a level of proteome coverage not previously realized for ultra-small sample loadings, and is expected to facilitate the analysis of subnanogram samples, including single mammalian cells. [ABSTRACT FROM AUTHOR]

Pseudomonas aeruginosa is a gram-negative pathogen, which causes life-threatening infections in immunocompromized patients. These bacteria express a secreted lipoxygenase (PA-LOX), which oxygenates free arachidonic acid to 15S-hydro(pero)xyeicosatetraenoic acid. It binds phospholipids at its active site and physically interacts with lipid vesicles. When incubated with red blood cells membrane lipids are oxidized and hemolysis is induced but the structures of the oxygenated membrane lipids have not been determined. Using a lipidomic approach, we analyzed the formation of oxidized phospholipids generated during the in vitro incubation of recombinant PA-LOX with human erythrocytes and cultured human lung epithelial cells. Precursor scanning of lipid extracts prepared from these cells followed by multiple reaction monitoring and MS/MS analysis revealed a complex mixture of oxidation products. For human red blood cells this mixture comprised forty different phosphatidylethanolamine and phosphatidylcholine species carrying oxidized fatty acid residues, such as hydroxy-octadecadienoic acids, hydroxy- and keto-eicosatetraenoic acid, hydroxy-docosahexaenoic acid as well as oxygenated derivatives of less frequently occurring polyenoic fatty acids. Similar oxygenation products were also detected when cultured lung epithelial cells were employed but here the amounts of oxygenated lipids were smaller and under identical experimental conditions we did not detect major signs of cell lysis. However, live imaging indicated an impaired capacity for trypan blue exclusion and an augmented mitosis rate. Taken together these data indicate that PA-LOX can oxidize the membrane lipids of eukaryotic cells and that the functional consequences of this reaction strongly depend on the cell type. [ABSTRACT FROM AUTHOR]

Imidacloprid is a neonicotinoid insecticide acting as an agonist of nicotinic acetylcholine receptors (nAChRs) in the target insects. However, questions about the safety to mammals, including human have emerged. Overactivation of mammalian peripheral catecholaminergic systems leads to onset of tachycardia, hypertension, vomiting, etc., which have been observed in acutely imidacloprid-poisoned patients as well. Physiological activation of the nAChRs is known to drive catecholamine biosynthesis and secretion in mammalian adrenal chromaffin cells. Yet, the impacts of imidacloprid on the catecholaminergic function of the chromaffin cells remain to be evaluated. In this study using PC12D cells, a catecholaminergic cell line derived from the medulla chromaffin-cell tumors of rat adrenal gland, we examined whether imidacloprid itself could impact the catecholamine-synthesizing ability. Imidacloprid alone did facilitate tyrosine hydroxylase (TH) transcription via activation of α3β4 nAChR and the α7 subunit-comprising receptor. The insecticide showed the TH transcription-facilitating ability at the concentrations of 3 and 30 μM, at which acetylcholine is known to produce physiological responses, including catecholamine secretion through the nAChRs in adrenal chromaffin cells. The insecticide-facilitated TH transcription was also dependent on PKA- and RhoA-mediated signaling pathways. The insecticide coincidentally raised levels of TH and phenylethanolamine N -methyltransferase (PNMT) mRNA, and as a consequence, increased catecholamine production, although the efficacy of the neonicotinoid was lesser than that of nicotine, indicating its partial agonist-like action. Intriguingly, in cultured rat adrenal chromaffin cells, imidacloprid did increase levels of TH and PNMT protein. When the chromaffin cells were treated with nicotine in the presence of the insecticide, nicotine-elevated adrenaline production was enhanced due to facilitation of nicotine-increased TH and PNMT protein expression, and simultaneous enhancement of nicotine-elevated adrenaline secretion also took place. These findings thus suggest that imidacloprid may facilitate the physiological functions of adrenal glands in mammals. [ABSTRACT FROM AUTHOR]

Recursive time series models are developed in this work for a fed-batch mammalian cell culture producing monoclonal antibodies, with key culture variables measured at different sampling frequencies. Glucose and glutamine feed rates are considered as inputs. A composite of an autoregressive moving average with exogenous input model and a dual rate-autoregressive with exogenous input model is used. Appropriate parameter constraints are imposed in parameter estimation algorithms and stability of these is examined and ensured. The data required for parameter estimation are generated from simulated fed-batch experiments using a well-tested first principles model. The predictions for glucose, glutamine, and viable cell concentrations track very well the data for these, with the errors for the high prediction horizons considered being limited to 10% or less. The prediction accuracy can be increased further if data from prior experiments with dynamic similarities are available. The models can be used reliably for model predictive control. [ABSTRACT FROM AUTHOR]

Calcium (Ca 2 + ) controls progression through the mammalian cell cycle by engaging a diverse range of molecular pathways. While the essential role of spatio-temporal Ca 2 + signalling in the cell cycle is well established, the precise mechanisms by which it regulates cell cycle entry and progression through G 1 are not particularly well understood. Here, high-resolution label-free semi-quantitative nLC-MS/MS analysis has been used to support a highly reproducible unbiased analysis of Ca 2 + influx dependent growth factor induced protein expression early in G 1 in human fibroblasts. Using this strategy a panel of 182 proteins whose expression was Ca 2 + dependent were identified. Pathway analysis has indicated that Ca 2 + likely regulates cell proliferation via PI3K/AKT pathway and its downstream target mTOR. In addition to cell proliferation found proteins were involved in the regulation of cell morphology and cellular assembly and organization, the environmental clues, which are known to regulate G 1 progression. Reported here data represents one of the most comprehensive proteomic datasets of growth factor and Ca 2 + dependent protein expression in the mammalian cell cycle and provides a rich source of publically available data to support continued investigation of the role of Ca 2 + in G 1 progression at both the molecular and systems level. Biological significance The results of this study provide new insight into Ca 2 + dependent regulation of cell cycle. This manuscript reports first to date global analysis of Ca 2 + regulated protein expression changes early in G 1 in non-transformed human fibroblast cell line. It also highlights canonical signalling pathways and biological processes that are regulated by the inhibition of Ca 2 + influx. Importantly, it appears that Ca 2 + may be the factor that links cell division with environmental cues, cell morphology and cellular assembly and organization, on which cell proliferation depends. Hence, the findings presented here provide numerous opportunities for more detailed investigations of the mechanism of Ca 2 + dependent regulation of cell cycle at the molecular and systemic level. [ABSTRACT FROM AUTHOR]

Overexpression of γ-tubulin leads to the formation of filaments, but nothing is known about such filaments with regard to possible presence in cells, structure and probable dynamics. Here, we used mammalian cell lines to investigate the ability of γ-tubulin to form filaments. We found that γ-tubulin produces fibers called γ-tubules in a GTP-dependent manner and that γ-tubules are made up of pericentrin and the γ-tubulin complex proteins 2, 3, 5 and 6. Furthermore, we noted that the number of cells with cytosolic γ-tubules is increased in non-dividing cells. Our experiments showed that γ-tubules are polar structures that have a low regrowth rate compared to microtubules. Also, we observed that γ-tubules were disassembled by treatment with cold, colcemid, citral dimethyl acetal, dimethyl fumarate or mutation of γ-tubulin GTPase domain, but were increased in number by treatment with taxol or by stable expression of the γ-tubulin 1–333 GTPase domain. Our results demonstrate that γ-tubulin forms filaments, and such assembly is facilitated by the GTPase domain of γ-tubulin. [ABSTRACT FROM AUTHOR]

Bleomycin (BLM) is an antibiotic isolated from Streptomyces verticillus . It has radiomimetic actions on DNA thus it has been widely used in clinical chemotherapy for the treatment of different types of cancer, including head and neck tumors, lymphomas, squamous-cell carcinomas and germ-cell tumors. Because of this, the study of BLM genotoxicity is of practical interest. This antibiotic is an S-independent clastogen and an agent that generates free radicals and induces single- and double-strand breaks in DNA. In the present review, we will summarize our current knowledge concerning the DNA and chromosome damage induced by BLM in mammalian cells, with emphasis on new developments published since 1991. [ABSTRACT FROM AUTHOR]

The Rvb1–Rvb2–Tah1–Pih1/prefoldin-like (R2TP/PFDL) complex is a unique chaperone that provides a platform for the assembly and maturation of many key multiprotein complexes in mammalian cells. Here, we propose to rename R2TP/PFDL as PAQosome ( p article for a rrangement of q uaternary structure) to more accurately represent its unique function. [ABSTRACT FROM AUTHOR]

Diacylglycerol kinase (DGK) phosphorylates diacylglycerol (DG) to produce phosphatidic acid (PA). Mammalian DGK comprises ten isozymes (α–κ) and regulates a wide variety of physiological and pathological events, such as cancer, type II diabetes, neuronal disorders and immune responses. DG and PA consist of various molecular species that have different acyl chains at the sn -1 and sn -2 positions, and consequently, mammalian cells contain at least 50 structurally distinct DG/PA species. Because DGK is one of the components of phosphatidylinositol (PI) turnover, the generally accepted dogma is that all DGK isozymes utilize 18:0/20:4-DG derived from PI turnover. We recently established a specific liquid chromatography-mass spectrometry method to analyze which PA species were generated by DGK isozymes in a cell stimulation-dependent manner. Interestingly, we determined that DGKδ, which is closely related to the pathogenesis of type II diabetes, preferentially utilized 14:0/16:0-, 14:0/16:1-, 16:0/16:0-, 16:0/16:1-, 16:0/18:0- and 16:0/18:1-DG species ( X : Y = the total number of carbon atoms: the total number of double bonds) supplied from the phosphatidylcholine-specific phospholipase C pathway, but not 18:0/20:4-DG, in high glucose-stimulated C2C12 myoblasts. Moreover, DGKα mainly consumed 14:0/16:0-, 16:0/18:1-, 18:0/18:1- and 18:1/18:1-DG species during cell proliferation in AKI melanoma cells. Furthermore, we found that 16:0/16:0-PA was specifically produced by DGKζ in Neuro-2a cells during retinoic acid- and serum starvation-induced neuronal differentiation. These results indicate that DGK isozymes utilize a variety of DG molecular species derived from PI turnover-independent pathways as substrates in different stimuli and cells. DGK isozymes phosphorylate various DG species to generate various PA species. It was revealed that the modes of activation of conventional and novel protein kinase isoforms by DG molecular species varied considerably. However, PA species-selective binding proteins have not been found to date. Therefore, we next attempted to identify PA species-selective binding proteins from the mouse brain and identified α-synuclein, which has causal links to Parkinson's disease. Intriguingly, we determined that among phospholipids, including several PA species (16:0/16:0-PA, 16:0/18:1-PA, 18:1/18:1-PA, 18:0/18:0-PA and 18:0/20:4-PA); 18:1/18:1-PA was the most strongly bound PA to α-synuclein. Moreover, 18:1/18:1-PA strongly enhanced secondary structural changes from the random coil form to the α-helix form and generated a multimeric and proteinase K-resistant α-synuclein protein. In contrast with the dogma described above, our recent studies strongly suggest that PI turnover-derived DG species and also various DG species derived from PI turnover-independent pathways are utilized by DGK isozymes. DG species supplied from distinct pathways may be utilized by DGK isozymes based on different stimuli present in different types of cells, and individual PA molecular species would have specific targets and exert their own physiological functions. [ABSTRACT FROM AUTHOR]

A diverse natural product-like (NPL) synthetic abietane diterpenoid library containing 86 compounds were obtained and the SARs were studied based on their antibacterial potential. Further in vitro cytotoxic and in silico drug-like properties evaluation showed that the potent antibacterial compound 84 had good drug-like properties and displayed low cytotoxicity toward noncancerous mammalian cells, indicating the study of AA and DHAA might be a good starting point for the search of novel antimicrobial molecules. Future work should be focused on the optimization of their potency and selectivity. [ABSTRACT FROM AUTHOR]