Molecular evaluation of the metabolism of estrogenic di(2-ethylhexyl) phthalate in Mycolicibacterium sp.

Cyanobacteria are prokaryotic organisms with wide morphological and metabolic diversity. By means of photosynthesis, they convert inorganic compounds into biomolecules, which may have commercial interest. In this work, we evaluated 20 cyanobacterial strains regarding their physiological aspects such as growth, photosynthesis and biochemical composition, some of which are revealed here for the first time. The organisms were cultivated in cylindrical photobioreactors (CPBR) for 144 h and the biomass was obtained. The light inside cultures was constant throughout experimental time and maintained at the saturation irradiance (Ik) of each species. Culture pH was maintained within 7.8 and 8.4 by automatic CO2 bubbling. Growth rate, dry biomass, chlorophyll a, carotenoids, phycocyanin, proteins, carbohydrates, lipids, polyhydroxyalkanoate (PHA) and antioxidant activity were determined. The proportionality of the biochemical composition varied among species, as well as the growth rates. Leptolyngbya sp. and Nostoc sp. (CCIBt3249) showed growth rates in the range of 0.7–0.8 d−1, followed by Rhabdorderma sp. (~ 0.6 d−1), and Phormidium sp. (~ 0.5 d−1). High carotenoid content was obtained in Rhabdoderma sp. (4.0 μg mL−1) and phycocyanin in Leptolyngbya sp. (60 μg mL−1). Higher total proteins were found in the genus Geitlerinema (75% DW), carbohydrates in Microcystis navacekii (30% DW) and lipids in Phormidium sp. (15% DW). Furthermore, Aphanocapsa holsatica showed the highest antioxidant activity (65%) and Sphaerocavum brasiliense, Microcystis aeruginosa, Nostoc sp. (CCIBt3249) and A. holsatica higher levels of PHA (~ 2% DW). This study reports on the biochemical composition of cyanobacteria that can impact the biotechnology of their production, highlighting potential strains with high productivity of specific biomolecules.     

Proteins and metabolites fingerprints of gestational diabetes mellitus forming protein–metabolite interactomes are its potential biomarkers

Gestational diabetes mellitus (GDM) is a consequence of glucose intolerance with an inadequate production of insulin that happens during pregnancy and leads to adverse health consequences for both mother and fetus. GDM patients are at higher risk for preeclampsia, and developing diabetes mellitus type 2 in later life, while the child born to GDM mothers are more prone to macrosomia, and hypoglycemia. The universally accepted diagnostic criteria for GDM are lacking, therefore there is a need for a diagnosis of GDM that can identify GDM at its early stage (first trimester). We have reviewed the literature on proteins and metabolites fingerprints of GDM. Further, we have performed protein–protein, metabolite–metabolite, and protein–metabolite interaction network studies on GDM proteins and metabolites fingerprints. Notably, some proteins and metabolites fingerprints are forming strong interaction networks at high confidence scores. Therefore, we have suggested that those proteins and metabolites that are forming protein–metabolite interactomes are the potential biomarkers of GDM. The protein–metabolite biomarkers interactome may help in a deep understanding of the prognosis, pathogenesis of GDM, and also detection of GDM. The protein–metabolites interactome may be further applied in planning future therapeutic strategies to promote long-term health benefits in GDM mothers and their children.     

Evolution of the folding landscape of effector caspases

Caspases are a family of cysteinyl proteases that control programmed cell death and maintain homeostasis in multicellular organisms. The caspase family is an excellent model to study protein evolution because all caspases are produced as zymogens (procaspases [PCPs]) that must be activated to gain full activity; the protein structures are conserved through hundreds of millions of years of evolution; and some allosteric features arose with the early ancestor, whereas others are more recent evolutionary events. The apoptotic caspases evolved from a common ancestor (CA) into two distinct subfamilies: monomers (initiator caspases) or dimers (effector caspases). Differences in activation mechanisms of the two subfamilies, and their oligomeric forms, play a central role in the regulation of apoptosis. Here, we examine changes in the folding landscape by characterizing human effector caspases and their CA. The results show that the effector caspases unfold by a minimum three-state equilibrium model at pH 7.5, where the native dimer is in equilibrium with a partially folded monomeric (PCP-7, CA) or dimeric (PCP-6) intermediate. In comparison, the unfolding pathway of PCP-3 contains both oligomeric forms of the intermediate. Overall, the data show that the folding landscape was first established with the CA and was retained for >650 million years. Partially folded monomeric or dimeric intermediates in the ancestral ensemble provide mechanisms for evolutionary changes that affect stability of extant caspases. The conserved folding landscape allows for the fine-tuning of enzyme stability in a species-dependent manner while retaining the overall caspase–hemoglobinase fold.     

Crystallographic analysis of synechocystis cyanoglobin reveals the structural changes accompanying ligand binding in a hexacoordinate hemoglobin

The crystal structures of cyanide and azide-bound forms of the truncated hemoglobin from Synechocystis are presented at 1.8 angstroms resolution. A comparison with the structure of the endogenously liganded protein reveals a conformational shift unprecedented in hemoglobins, and provides the first picture of a hexacoordinate hemoglobin in both the bis-histidyl and the exogenously coordinated states. The structural changes between the different conformations are confined to two regions of the protein; the B helix, and the E helix, including the EF loop. A molecular "hinge" controlling movement of the E helix is observed in the EF loop, which is composed of three principal structural elements: Arg64, the heme-d-propionate, and a three-residue extension of the F helix. Additional features of the structural transition between the two protein conformations are discussed as they relate to the complex ligand-binding behavior observed in hexacoordinate hemoglobins, and the potential physiological function of this class of proteins.     

Ligand-induced assembling of the type I interferon receptor on supported lipid bilayers

Type I interferons (IFNs) elicit antiviral, antiproliferative and immuno-modulatory responses through binding to a shared receptor consisting of the transmembrane proteins ifnar1 and ifnar2. Differential signaling by different interferons, in particular IFNalphas and IFNbeta, suggests different modes of receptor engagement. Using reflectometric interference spectroscopy (RIfS), we studied kinetics and affinities of the interactions between IFNs and the extracellular receptor domains of ifnar1 (ifnar1-EC) and ifnar2 (ifnar2-EC). For IFNalpha2, we determined a K(D) value of 3 nM and 5 microM for the interaction with ifnar2-EC and ifnar1-EC, respectively. As compared to IFNalpha2, IFNbeta formed complexes with ifnar2-EC as well as ifnar1-EC with substantially higher affinity. For neither IFNalpha2 nor IFNbeta was stabilization of the complex with ifnar1-EC in the presence of soluble ifnar2-EC observed. We investigated ligand-induced complex formation with ifnar1-EC and ifnar2-EC being tethered onto solid-supported, fluid lipid bilayers by RIfS and total internal reflection fluorescence spectroscopy. We observed very stable binding of IFNalpha2 at high receptor surface concentrations with an apparent k(d) value approximately 200 times lower than that for ifnar2-EC alone. The apparent k(d) value was strongly dependent on the surface concentration of the receptor components, suggesting kinetic stabilization. This was corroborated by the fast exchange of labeled IFNalpha2 bound to the receptor by unlabeled IFNalpha2. Taken together, our results indicate that IFN first binds to ifnar2 and subsequently recruits ifnar1 in a transient fashion. In particular, this second step is much more efficient for IFNbeta than for IFNalpha2, which could explain differential activities observed for these IFNs.     

Identifying control mechanisms of granuloma formation during M. tuberculosis infection using an agent-based model

Infection with Mycobacterium tuberculosis is a major world health problem. An estimated 2 billion people are presently infected and the disease causes approximately 3 million deaths per year. After bacteria are inhaled into the lung, a complex immune response is triggered leading to the formation of multicellular structures termed granulomas. It is believed that the collection of host granulomas either contain bacteria resulting in a latent infection or are unable to do so, leading to active disease. Thus, understanding granuloma formation and function is essential for improving both diagnosis and treatment of tuberculosis. Granuloma formation is a complex spatio-temporal system involving interactions of bacteria, specific immune cells, including macrophages, CD4+ and CD8+ T cells, as well as immune effectors such as chemokine and cytokines. To study this complex dynamical system we have developed an agent-based model of granuloma formation in the lung. This model combines continuous representations of chemokines with discrete agent representations of macrophages and T cells in a cellular automata-like environment. Our results indicate that key host elements involved in granuloma formation are chemokine diffusion, prevention of macrophage overcrowding within the granuloma, arrival time, location and number of T cells within the granuloma, and an overall host ability to activate macrophages. Interestingly, a key bacterial factor is its intracellular growth rate, whereby slow growth actually facilitates survival.     

Integrated coastal management in the Venice lagoon and its watershed

The Venice Lagoon (VL) is a complex ecosystem in which public participation and area-based management has often been neglected by administrative bodies involved in the planning of coastal projects and public works. In this area, the analysis of the local situation highlighted a substantial absence of coordination among the various administrative bodies in charge of planning and management at various governmental levels and in different regulated economic sectors. This paper analyses public participation and collaboration with reference to the Integrated Coastal Management context (ICM). The paper examines specific requirements, constraints, and opportunities for the complex case of the VL where participatory management and institutional coordination need enhancement.     

Expression and characterization of human malaria parasite Plasmodium falciparum origin recognition complex subunit 1

In eukaryotes, the origin recognition complex (ORC) is essential for the initiation of DNA replication. The largest subunit of this complex (ORC1) has a regulatory role in origin activation. Here we report the cloning and functional characterization of Plasmodium falciparum ORC1 homolog. Using immunofluorescence and immunoelectron microscopy, we show here that PfORC1 is expressed in the nucleus during the late trophozoite and schizont stages where maximum amount of DNA replication takes place. Homology modelling of the carboxy terminal region of PfORC1 (781-1033) using Saccharomyces pombe Cdc6/Cdc18 homolog as a template reveals the presence of a similar AAA+ type nucleotide-binding fold. This region shows ATPase activity in vitro that is important for the origin activity. To our knowledge, this is the first evidence of an individual ORC subunit that shows ATPase activity. These observations strongly suggest that PfORC1 might be involved in DNA replication initiation during the blood stage of the parasitic life cycle.