The evolution of the Ecdysozoa

Ecdysozoa is a clade composed of eight phyla: the arthropods, tardigrades and onychophorans that share segmentation and appendages and the nematodes, nematomorphs, priapulids, kinorhynchs and loriciferans, which are worms with an anterior proboscis or introvert. Ecdysozoa contains the vast majority of animal species and there is a great diversity of body plans among both living and fossil members. The monophyly of the clade has been called into question by some workers based on analyses of whole genome datasets. We review the evidence that now conclusively supports the unique origin of these phyla. Relationships within Ecdysozoa are also controversial and we discuss the molecular and morphological evidence for a number of monophyletic groups within this superphylum.     

Molecular modeling and experimental evidence for hypericin as a substrate for mitochondrial complex III; mitochondrial photodamage as demonstrated using specific inhibitors

The effect of hypericin photoactivation on mitochondria of human prostate carcinoma cells was studied using a range of mitochondrial inhibitors. Oligomycin significantly enhanced hypericin phototoxicity while atractyloside and antymicin A conferred a significant protection. Use of myxothiazol did not affect cell survival following hypericin photoactivation. These results signify a protective role for F(1)F(0)-ATP synthase running in reverse mode, and a significant photodamage at the quinone-reducing site of mitochondrial complex III. In light of these results, we performed molecular modeling of hypericin binding to complex III. This revealed three binding sites, two of which coincided with the quinol-oxidizing and quinone-reducing centers. Using submitochondrial particles we examined hypericin as a possible substrate of complex III and compared this to its natural substrate, ubiquinone-10. Our results demonstrate uniquely that hypericin is an efficient substrate for complex III, and this activity is inhibited by myxothiazol and antimycin A. We further demonstrated that hypericin photosensitization completely inactivated complex III with ubiquinone as substrate. The ability to enhance HYP potency by inhibition of F(1)F(0)-ATP synthase or depress HYP efficacy by inhibition at the Qi site of complex III provides a potential to increase the therapeutic index of HYP and amplify its PDT action in tumor cells.     

Synthesis, spectroscopic, structural and electrochemical studies of carboxyl substituted 1,4-naphthoquinones

Two carboxyl substituted quinones and their ethyl esters were prepared by alkylation of 2-methyl-1,4-naphthoquinone (MNQ), also known as menadione or vitamin K₃. All products were characterized by spectroscopic (¹H NMR, ¹³C NMR, IR) and electrochemical (cyclic voltammetry) methods, and the crystal structure of the two carboxylic derivatives was also determined. Both carboxyl substituted quinones crystallize in the system as hydrogen bonded dimers. In MeCN, the cyclic voltammograms of the ester derivatives present two reversible one-electron redox waves very similar to those of the parent quinone, MNQ. However, in the same solvent, the corresponding carboxyl substituted quinones show one cathodic and one anodic additional irreversible waves at more positive potentials and a decrease in current intensity of the two quinone reduction waves accompanied by loss of the quasi-reversible character of the second wave. These results show that the presence of the carboxylic substituent does not greatly modify the redox behaviour of the quinone, except for a small anodic shift of the potentials, but the associated presence of H⁺ ions in solution causes an important perturbation to the system, stabilizing the electrogenerated semiquinones by intermolecular self-protonation and/or hydrogen bonding.     

Modelling potential habitat of the invasive ctenophore <Emphasis Type="Italic">Mnemiopsis leidyi</Emphasis> in Aegean Sea

The invasive ctenophore Mnemiopsis leidyi was accidentally introduced into the Black Sea in the early 1980s and it was first sighted in the Aegean Sea (Eastern Mediterranean) in the early 1990s. This article presents a first attempt to develop a predictive spatial model based on M. leidyi presence data and satellite environmental data from the Aegean Sea during early summer, in order to identify those areas in the Greek Seas and the entire Mediterranean basin that could serve as potential habitat for the species. Generalized additive models (GAM) were applied. The final GAM model indicated higher probability of finding M. leidyi present in depths of 65–135 m and sea surface temperature values of 21–25°C. Furthermore, the significant interaction between photosynthetically active radiation (PAR) and sea level anomaly (SLA) indicated a higher probability of M. leidyi presence in low values of PAR and SLA. In the next step, the final GAM was applied in a prediction grid of mean monthly satellite values for June 2004–2006 in order to estimate probability of M. leidyi presence in the Hellenic Seas and the whole Mediterranean basin at a GIS resolution of 4 km. In the Aegean Sea, species potential habitat included areas influenced by the Black Sea Water (e.g. Thracian Sea, Limnos-Imvros plateau), gulfs that are affected by river runoffs, such as the Thermaikos, Strymonikos and Patraikos gulfs, or areas with strong anthropogenic influence such as the Saronikos gulf. Areas with the same environmental conditions as those in Aegean Sea have been indicated in certain spots of the Levantine Sea as well as in coastal waters of Egypt and Libya, although their spatial extent varied largely among years examined. However, the occurrence of conditions that are linked to high probability of M. leidyi presence does not necessarily mean that these areas can support successful reproduction, high population or bloom levels, since these depend on a combination of temperature, salinity, food availability and the abundance of predators. Guest editor: V. D. Valavanis Essential Fish Habitat Mapping in the Mediterranean     

Development and characterization of a tissue engineered pancreatic substitute based on recombinant intestinal endocrine L‐cells

A tissue engineered pancreatic substitute (TEPS) consisting of insulin‐producing cells appropriately designed and encapsulated to support cellular function and prevent interaction with the host may provide physiological blood glucose regulation for the treatment of insulin dependent diabetes (IDD). The performance of agarose‐based constructs which contained either a single cell suspension of GLUTag‐INS cells, a suspension of pre‐aggregated GLUTag‐INS spheroids, or GLUTag‐INS cells on small intestinal submucosa (SIS), was evaluated in vitro for total cell number, weekly glucose consumption and insulin secretion rates (GCR and ISR), and induced insulin secretion function. The three types of TEPS studied displayed similar number of cells, GCR, and ISR throughout 4 weeks of culture. However, the TEPS, which incorporated SIS as a substrate for the GLUTag‐INS cells, was the only type of TEPS tested which was able to retain the induced insulin secretion function of non‐encapsulated GLUTag‐INS cells. Though improvements in the expression level of GLUTag‐INS cells and/or the number of viable cells contained within the TEPS are needed for successful treatment of a murine model of IDD, this study has revealed a potential method for promoting proper cellular function of recombinant L‐cells upon incorporation into an implantable three‐dimensional TEPS. Biotechnol. Bioeng. 2009;103: 828–834. © 2009 Wiley Periodicals, Inc.     

The Mechanism of CSF-1-induced Wiskott-Aldrich Syndrome Protein Activation in Vivo: A ROLE FOR PHOSPHATIDYLINOSITOL 3-KINASE AND Cdc42*

A role for Wiskott-Aldrich syndrome protein (WASP) in chemotaxis to various agents has been demonstrated in monocyte-derived cell types. Although WASP has been shown to be activated by multiple mechanisms in vitro, it is unclear how WASP is regulated in vivo. A WASP biosensor (WASPbs), which uses intramolecular fluorescence resonance energy transfer to report WASP activation in vivo, was constructed, and following transfection of macrophages, activation of WASPbs upon treatment with colony-stimulating factor-1 (CSF-1) was detected globally as early as 30 s and remained localized to protrusive regions at later time points. Similar results were obtained when endogenous WASP activation was determined using conformation-sensitive antibodies. In vivo CSF-1-induced WASP activation was fully Cdc42-dependent. Activation of WASP in response to treatment with CSF-1 was also shown to be phosphatidylinositol 3-kinase-dependent. However, treatment with the Src family kinase inhibitors PP2 or SU6656 or disruption of the major tyrosine phosphorylation site of WASPbs (Y291F mutation) did not reduce the level of CSF-1-induced WASP activation. Our results indicate that WASP activation downstream of CSF-1R is phosphatidylinositol 3-kinase- and Cdc42-dependent consistent with an involvement of these molecules in macrophage migration. However, although tyrosine phosphorylation of WASP has been proposed to stimulate WASP activity, we found no evidence to indicate that this occurs in vivo.Macrophages, terminally differentiated cells of the mononuclear phagocytic lineage, are found throughout the body and play important roles in normal tissue development and immune defense. However, in certain circumstances, excessive recruitment of macrophages has been shown to participate in the progression of several diseases, inflammatory (rheumatoid arthritis) or metabolic (atherosclerosis), as well as in tumor progression (1–3). Importantly expression of colony-stimulating factor-1 (CSF-1),⁴ the most pleiotropic macrophage growth factor, has been correlated with the progression of these disease states (for a review, see Ref. 4). Inhibition of undesirable macrophage recruitment to specific sites in response to CSF-1 is therefore an attractive goal for therapies (5).In addition to stimulating survival, proliferation, and differentiation of monocytes and macrophages, CSF-1 is also a potent chemotactic factor inducing the migration of these cell types (for a review, see Ref. 4). CSF-1 stimulation leads to the rapid production of F-actin-rich protrusions and the spreading and migration of macrophages (4). All CSF-1 effects are mediated through its tyrosine kinase receptor (CSF-1R), which upon activation leads to phosphorylation of tyrosine residues in a number of signaling molecules. Downstream molecules essential for macrophage migration in response to CSF-1 include phosphatidylinositol 3-kinase (PI3K) isoforms β and δ (6, 7). PI3K may potentially regulate migration through the activation of guanine nucleotide exchange factor activity to Rac1 and Cdc42, which are required for CSF-1-elicited protrusions (8, 9) and chemotaxis (10). The major means by which Rac and Cdc42 regulate the Arp2/3 complex is through the Wiskott-Aldrich syndrome protein/Wiskott-Aldrich syndrome verprolin-homologous (WASP/WAVE) family of proteins (11). A Rac1-IRSp53-Abi1-WAVE2 complex has been shown to mediate CSF-1-induced macrophage motility (12, 13), and a unique role for WASP in macrophage chemotaxis to CSF-1, formylmethionylleucylphenylalanine, MCP-1, and MIP-1α has been demonstrated (14, 15). WASP is a hematopoietic cell-specific regulator of Arp2/3-dependent actin remodeling. The catalytically active domain of WASP lies in its C terminus, which is conserved among all WASP/WAVE proteins and contains a VCA (verprolin homology, cofilin-like, and acidic region) domain capable of activating the Arp2/3 complex. The other domains found in WASP can regulate, directly or indirectly, the activity of its VCA domain (for a review, see Ref. 16). Both WASP and N-WASP bind activated Cdc42 through their GTPase-binding domain, which is believed to cause a structural transition that results in dissociation of the intramolecular contacts leaving the VCA domain accessible for Arp2/3 binding (17, 18). In addition, biochemical studies have revealed that several signaling molecules, including WASP-interacting SH3 protein, WASP-interacting protein, Grb2, phosphoinositides, and Src family kinases, activate N-WASP (for reviews, see Refs. 16 and 19). Phosphorylation of WASP has also been proposed to activate Arp2/3-mediated actin polymerization in vitro (20–22).Recently different probes have been developed that detect a conformational change in N-WASP and therefore reflect its activation (23–25). Using either a fluorescence resonance energy transfer (FRET)-based biosensor that detects a conformational change in N-WASP (23, 24) or antibodies that can only bind to the open conformation of N-WASP (25), N-WASP has been shown to be activated in response to epidermal growth factor in HEK293 cells and in MTLn3 carcinoma cells. This activity has been temporally localized to subcellular compartments important for carcinoma cell chemotaxis and invasion (24). We have adapted these approaches to explore the signal transduction pathways responsible for the activation of WASP in vivo.     

A Unitary Anesthetic Binding Site at High Resolution

Propofol is the most widely used injectable general anesthetic. Its targets include ligand-gated ion channels such as the GABA_A receptor, but such receptor-channel complexes remain challenging to study at atomic resolution. Until structural biology methods advance to the point of being able to deal with systems such as the GABA_A receptor, it will be necessary to use more tractable surrogates to probe the molecular details of anesthetic recognition. We have previously shown that recognition of inhalational general anesthetics by the model protein apoferritin closely mirrors recognition by more complex and clinically relevant protein targets; here we show that apoferritin also binds propofol and related GABAergic anesthetics, and that the same binding site mediates recognition of both inhalational and injectable anesthetics. Apoferritin binding affinities for a series of propofol analogs were found to be strongly correlated with the ability to potentiate GABA responses at GABA_A receptors, validating this model system for injectable anesthetics. High resolution x-ray crystal structures reveal that, despite the presence of hydrogen bond donors and acceptors, anesthetic recognition is mediated largely by van der Waals forces and the hydrophobic effect. Molecular dynamics simulations indicate that the ligands undergo considerable fluctuations about their equilibrium positions. Finally, apoferritin displays both structural and dynamic responses to anesthetic binding, which may mimic changes elicited by anesthetics in physiologic targets like ion channels.Most general anesthetics alter the activity of ligand-gated ion channels, and electrophysiology, photolabeling, and transgenic animal experiments imply that this effect contributes to the mechanism of anesthesia (1–9). Although the molecular mechanism for this effect is not yet clear, photolabeling studies indicate that anesthetics bind within the transmembrane regions of Cys-loop ligand-gated ion channels such as the nicotinic acetylcholine and the γ-aminobutyric acid (GABA)² type A receptors (2, 9–11). Practical difficulties associated with overexpression, purification, and crystallization of ion channels have thus far stymied investigation of the structural and energetic bases underlying anesthetic recognition. However, general anesthetics also bind specifically to sites in soluble proteins, including firefly luciferase, human serum albumin (HSA), and horse spleen apoferritin (HSAF) (12–14), and x-ray crystal structures have been determined for complexes of these proteins with several general anesthetics (14–16). In particular, HSAF is an attractive model for studying anesthetic-protein interactions because it has the highest affinity for anesthetics of any protein studied to date, has a unique anesthetic binding site, and is a multimer of 4-helix bundles, much like the putative anesthetic binding regions in ligand-gated channels. In addition, apoferritin is commercially available and crystallizes readily. Most importantly, however, the affinity of HSAF for a broad range of general anesthetics is highly correlated with anesthetic potency, confirming the utility and relevance of this model system (17).Ferritin is a 24-mer iron-binding protein. It sequesters free iron ions, thereby helping to maintain non-toxic levels of iron in the cell and functioning as a cellular iron reservoir (18, 19). Each subunit has a molecular mass of ∼20 kDa and adopts a 4-helix bundle fold. The 24-mer forms a hollow, roughly spherical particle with 432 symmetry. Two ferritin isoforms are found in mammals, heavy (H) and light (L), and 24-mers can contain all H chains, all L chains, or mixtures of varying stoichiometry; the biological significance of the H/L ratio is not yet clear (20).In addition to the large central cavity, the apoferritin 24-mer contains additional, smaller cavities at the dimer interfaces; these smaller cavities are of an appropriate size to accommodate anesthetics. X-ray crystallography has confirmed that this interfacial cavity is the binding site for the inhalational anesthetics halothane and isoflurane, and isothermal titration calorimetry (ITC) measurements have shown that this interfacial site has a relatively high affinity for these anesthetics (K_a values ∼10⁵ m⁻¹) (14).General anesthetics fall into at least two broad classes, inhalational and injectable. Whereas both classes of drugs can induce the amnesia, immobility, and hypnosis associated with anesthesia, molecules in the two classes differ substantially in their chemical and physical properties. Prior to this work, only one crystal structure has been available for an injectable general anesthetic complexed with a protein-propofol, bound to HSA (16). This structure revealed that the propofol binding sites on this protein do not, by and large, overlap with the binding sites for inhalational anesthetics. This raises the question of whether the two types of drug invariably bind to separate sets of targets, or whether they could possibly transduce their effects by binding to a single protein site. To address this question we assessed whether propofol binds to the apoferritin site that had been previously identified as the binding site for inhalational anesthetics. Using x-ray crystallography, calorimetry, and molecular modeling, we show that the two types of anesthetics do indeed share a common binding site. We also investigated structure-binding relationships for a homologous series of propofol-like compounds and found that, remarkably, the energetics of binding to apoferritin precisely match the compound''s abilities to potentiate GABA effects at GABA_A receptors, suggesting that similar structural and physicochemical factors mediate anesthetic recognition by both apoferritin and ligand-gated ion channels. This argues for the possibility that anesthetic binding might trigger structural and dynamic alterations in GABA_A receptors similar to those observed in apoferritin, and that these changes underlie anesthetic effects.     

Sirtuins at the crossroads of stemness,aging, and cancer

Sirtuins are stress‐responsive proteins that direct various post‐translational modifications (PTMs) and as a result, are considered to be master regulators of several cellular processes. They are known to both extend lifespan and regulate spontaneous tumor development. As both aging and cancer are associated with altered stem cell function, the possibility that the involvement of sirtuins in these events is mediated by their roles in stem cells is worthy of investigation. Research to date suggests that the individual sirtuin family members can differentially regulate embryonic, hematopoietic as well as other adult stem cells in a tissue‐ and cell type‐specific context. Sirtuin‐driven regulation of both cell differentiation and signaling pathways previously involved in stem cell maintenance has been described where downstream effectors involved determine the biological outcome. Similarly, diverse roles have been reported in cancer stem cells (CSCs), depending on the tissue of origin. This review highlights the current knowledge which places sirtuins at the intersection of stem cells, aging, and cancer. By outlining the plethora of stem cell‐related roles for individual sirtuins in various contexts, our purpose was to provide an indication of their significance in relation to cancer and aging, as well as to generate a clearer picture of their therapeutic potential. Finally, we propose future directions which will contribute to the better understanding of sirtuins, thereby further unraveling the full repertoire of sirtuin functions in both normal stem cells and CSCs.     

Modeling of single-cell oil production under nitrogen-limited and substrate inhibition conditions

Sweet sorghum extract was used as substrate for lipid accumulation by the oleaginous fungus Mortierella isabellina in batch cultures. Various initial sugar (13–91 g/L) and nitrogen (100–785 mg/L) concentrations resulting in various C/N (43–53) ratios were tested. Oil accumulation ranged between 43% and 51% corresponding to oil production from 2.2 to 9.3 g/L. A detailed mathematical model was developed. This model is able to adequately predict biomass growth, lipid accumulation, and sugar and nitrogen consumption. The model assumes that fungus growth is inhibited at high sugar concentrations. A set of kinetic experiments was used for model kinetic parameters estimation, while another set of experiments was used for model validation. The developed model could be generalized for similar systems of lipid accumulation and become a useful tool for reactor design for biofuel production. Bioeng. 2011; 108:1049–1055. © 2010 Wiley Periodicals, Inc.