Influence of production process design on inclusion bodies protein: the case of an Antarctic flavohemoglobin

Background  

Protein over-production in Escherichia coli often results in formation of inclusion bodies (IBs). Some recent reports have shown that the aggregation into IBs does not necessarily mean that the target protein is inactivated and that IBs may contain a high proportion of correctly folded protein. This proportion is variable depending on the protein itself, the genetic background of the producing cells and the expression temperature. In this paper we have evaluated the influence of other production process parameters on the quality of an inclusion bodies protein.     

Karyological evolution and systematics of Malagasy microhylid frogs

Microhylid frogs are a group of largely unresolved phylogeny, and diverse data sets are needed to improve the evolutionary understanding of these amphibians. We here report karyological data for 22 species of this family, belonging to the Malagasy genera Anodonthyla, Cophyla, Platypelis, Plethodontohyla, Rhombophryne, and Stumpffia (Cophylinae); Scaphiophryne and Paradoxophyla (Scaphiophryninae); and Dyscophus (Dyscophinae); and the Asian genera Calluella and Ramanella (Microhylinae). All species studied have 2n=26 chromosomes, most of which are metacentric or submetacentric. Chromosome morphology, banding pattern, and position of the nucleolar organizer regions (NORs) provide relevant characters for the understanding of the phylogeny and systematics of these frogs. The species of the Cophylinae are characterized by a subtelocentric or telocentric fourth chromosome pair (submetacentric only in Anodonthyla), which can be seen as a synapomorphy for this subfamily. Shifts in NOR position within the Cophylinae are frequent and agree with recent mitochondrial DNA data, corroborating the non-monophyly of the genus Plethodontohyla. Changes of NOR position and chromosome morphology (i.e., occurrence of subtelocentric and telocentric elements) were also common in this subfamily, possibly being related to their faster mitochondrial substitution rate and high species diversity. The ninth chromosome pair of the examined specimens of Dyscophus guineti, all juveniles, is heteromorphic. In this pair, one of the two chromosomes is longer due to the addition of two heterochromatic segments, raising the possibility that one chromosome of this pair may be a sex chromosome.     

A high-fat, ketogenic diet induces a unique metabolic state in mice

Ketogenic diets have been used as an approach to weight loss on the basis of the theoretical advantage of a low-carbohydrate, high-fat diet. To evaluate the physiological and metabolic effects of such diets on weight we studied mice consuming a very-low-carbohydrate, ketogenic diet (KD). This diet had profound effects on energy balance and gene expression. C57BL/6 mice animals were fed one of four diets: KD; a commonly used obesogenic high-fat, high-sucrose diet (HF); 66% caloric restriction (CR); and control chow (C). Mice on KD ate the same calories as mice on C and HF, but weight dropped and stabilized at 85% initial weight, similar to CR. This was consistent with increased energy expenditure seen in animals fed KD vs. those on C and CR. Microarray analysis of liver showed a unique pattern of gene expression in KD, with increased expression of genes in fatty acid oxidation pathways and reduction in lipid synthesis pathways. Animals made obese on HF and transitioned to KD lost all excess body weight, improved glucose tolerance, and increased energy expenditure. Analysis of key genes showed similar changes as those seen in lean animals placed directly on KD. Additionally, AMP kinase activity was increased, with a corresponding decrease in ACC activity. These data indicate that KD induces a unique metabolic state congruous with weight loss.     

Iron deficiency differently affects metabolic responses in soybean roots

Iron deficiency responses were investigated in roots of soybean, a Strategy I plant species. Soybean responds to iron deficiency by decreasing growth, both at the root and shoot level. Chlorotic symptoms in younger leaves were evident after a few days of iron deficiency, with chlorophyll content being dramatically decreased. Moreover, several important differences were found as compared with other species belonging to the same Strategy I. The main differences are (i) a lower capacity to acidify the hydroponic culture medium, that was also reflected by a lower H(+)-ATPase activity as determined in a plasma membrane-enriched fraction isolated from the roots; (ii) a drastically reduced activity of the phosphoenolpyruvate carboxylase enzyme; (iii) a decrease in both cytosolic and vacuolar pHs; (iv) an increase in the vacuolar phosphate concentration, and (v) an increased exudation of organic carbon, particularly citrate, phenolics, and amino acids. Apparently, in soybean roots, some of the responses to iron deficiency, such as the acidification of the rhizosphere and other related processes, do not occur or occur only at a lower degree. These results suggest that the biochemical mechanisms induced by this nutritional disorder are differently regulated in this plant. A possible role of inorganic phosphate in the balance of intracellular pHs is also discussed.     

Helper-dependent adenovirus for the gene therapy of proliferative retinopathies: stable gene transfer, regulated gene expression and therapeutic efficacy

BACKGROUND: Ocular neovascular disorders, such as diabetic retinopathy and age-related macular degeneration, are the principal causes of blindness in developed countries. Current treatments are of limited efficacy, whereas a therapy based on intraocular gene transfer of angiostatic factors represents a promising alternative. For the first time we have explored the potential of helper-dependent adenovirus (HD-Ad), the last generation of Ad vectors, in the therapy of retinal neovascularization. METHODS: We first analyzed efficiency and stability of intraretinal gene transfer following intravitreous injection in mice. A HD-Ad vector expressing green fluorescent protein (GFP) under the control of the cytomegalovirus (CMV) promoter (HD-Ad/GFP) was compared with a first-generation (E1/E3-deleted) Ad vector carrying an identical GFP expression cassette (FG-Ad/GFP). We also constructed HD-Ad vectors expressing a soluble form of the VEGF receptor (sFlt-1) in a constitutive (HD-Ad/sFlt-1) or doxycycline (dox)-inducible (HD-Ad/S-M2/sFlt-1) manner and tested their therapeutic efficacy upon intravitreous delivery in a rat model of oxygen-induced retinopathy (OIR). RESULTS: HD-Ad/GFP promoted long-lasting (up to 1 year) transgene expression in retinal Müller cells, in marked contrast with the short-term expression observed with FG-Ad/GFP. Intravitreous injection of HD-Ad vectors expressing sFlt-1 resulted in detectable levels of sFlt-1 and inhibited retinal neovascularization by more than 60% in a rat model of OIR. Notably, the therapeutic efficacy of the inducible vector HD-Ad/S-M2/sFlt-1 was strictly dox-dependent. CONCLUSIONS: HD-Ad vectors enable stable gene transfer and regulated expression of angiostatic factors following intravitreous injection and thus are attractive vehicles for the gene therapy of neovascular diseases of the retina.     

Cross-presentation of caspase-cleaved apoptotic self antigens in HIV infection

We found that the proteome of apoptotic T cells includes prominent fragments of cellular proteins generated by caspases and that a high proportion of distinct T cell epitopes in these fragments is recognized by CD8+ T cells during HIV infection. The frequencies of effector CD8+ T cells that are specific for apoptosis-dependent epitopes correlate with the frequency of circulating apoptotic CD4+ T cells in HIV-1-infected individuals. We propose that these self-reactive effector CD8+ T cells may contribute to the systemic immune activation during chronic HIV infection. The caspase-dependent cleavage of proteins associated with apoptotic cells has a key role in the induction of self-reactive CD8+ T cell responses, as the caspase-cleaved fragments are efficiently targeted to the processing machinery and are cross-presented by dendritic cells. These findings demonstrate a previously undescribed role for caspases in immunopathology.     

Use of cryopreserved transiently transfected cells in high-throughput pregnane X receptor transactivation assay

Cryopreserved, transiently transfected HepG2 cells were compared to freshly transfected HepG2 cells for use in a pregnane X receptor (PXR) transactivation assay. Assay performance was similar for both cell preparations; however, cryopreserved cells demonstrated less interassay variation. Validation with drugs of different PXR activation potencies and efficacies demonstrated an excellent correlation (r(2) > 0.95) between cryopreserved and fresh cells. Cryopreservation did not change the effect of known CYP3A4 inducers that have poor cell permeability, indicating that cryopreservation had little effect on membrane permeability. In addition, cryopreserved HepG2 cells did not exhibit enhanced susceptibility to cytotoxic compounds compared to transiently transfected control cells. The use of cryopreserved cells enables this assay to run with enhanced efficiency.     

Cloning and Biochemical Characterization of <Emphasis Type="Italic">ToFZY</Emphasis>, a Tomato Gene Encoding a Flavin Monooxygenase Involved in a Tryptophan-dependent Auxin Biosynthesis Pathway

Indole-3-acetic acid (IAA), the main endogenous auxin, has been known for decades to be a key regulator for plant growth and development. Multiple routes have been proposed for IAA biosynthesis but physiologic roles or relevance of the different routes are still unclear. Recently, four members of the Arabidopsis thaliana YUC gene family have been implicated in an additional requirement of IAA involved in floral organ and vascular tissue formation. The loss-of-function yuc1yuc4 double mutants in Arabidopsis displayed phenotypes similar to the previously described loss-of-function floozy mutants in petunia (fzy). Moreover, it has been demonstrated that YUC1 encodes a flavin monooxygenase (FMO) that catalyzes a rate-limiting step of a tryptophan-dependent auxin biosynthesis pathway: the conversion of tryptamine to N-hydroxyl-tryptamine. Here we report on the genetic study of ToFZY, the putative tomato ortholog of YUC4 and FZY, including gene and cDNA sequence comparison and a preliminary expression analysis. In addition, we describe a novel conserved amino acid motif that may be considered a hallmark potentially useful for the identification of new YUC-like FMOs. We also demonstrate that ToFZY encodes a protein with the same enzymatic activity as YUC1. Finally, we provide evidence suggesting that the ToFZY gene belongs to a multigenic family whose members may exhibit a temporal and spatial specialization similar to that described in A. thaliana.     

Contribution of two ionotropic purinergic receptors to ATP responses in submandibular gland ductal cells

The effect of extracellular ATP on salivary gland function was compared in wild-type (WT) and P2X(7) knockout (KO) mice. The increase in the intracellular concentration of calcium ([Ca(2+)](i)) in response to carbachol was similar in submandibular ductal cells of WT and KO mice. ATP and its analog, benzoyl-ATP, induced a sustained increase in the [Ca(2+)](i) in WT animals. In KO mice, ATP slightly and transiently increased the [Ca(2+)](i) and benzoyl-ATP had no effect. The response to ATP of WT but not KO mice was blocked by KN-62, Coomassie blue and magnesium. The small response of ATP observed in KO mice was completely blocked in the absence of extracellular calcium, unchanged by U73122 and potentiated by ivermectin indicating the probable involvement of a P2X(4) receptor. A RT-PCR and a Western blot confirmed the presence of these receptors in ducts of both WT and KO mice. ATP increased the permeability of the cells to ethidium bromide and stimulated a phospholipase A(2) activity in WT but not KO mice. Mice submandibular gland cells secreted IL-1beta but this secretion was not modified by ATP and was similar in both groups of animals. The volume of saliva provoked by pilocarpine and the concentration of proteins, sodium and chloride in this saliva was similar in both groups of animals. The concentration of potassium was higher in KO mice. We can conclude that the major purinergic receptors expressed in mice submandibular ductal cells are P2X(7) receptors but that P2X(4) receptors are also involved in some ATP effects.     

Structural risk minimization: a robust method for density-dependence detection and model selection

Statistically distinguishing density‐dependent from density‐independent populations and selecting the best demographic model for a given population are problems of primary importance. Traditional approaches are PBLR (parametric bootstrapping of likelihood ratios) and Information criteria (IC), such as the Schwarz information criterion (SIC), the Akaike information criterion (AIC) or the Final prediction error (FPE). While PBLR is suitable for choosing from a couple of models, ICs select the best model from among a set of candidates. In this paper, we use the Structural risk minimization (SRM) approach. SRM is the model selection criterion developed within the Statistical learning theory (SLT), a theory of great generality for modelling and learning with finite samples. SRM is almost unknown in the ecological literature and has never been used to analyze time series. First, we compare SRM with PBLR in terms of their ability to discriminate between the Malthusian and the density‐dependent Ricker model. We rigorously repeat the experiments described in a previous study and find out that SRM is equally powerful in detecting density‐independence and much more powerful in detecting density‐dependence. Then, we compare SRM against ICs in terms of their ability to select one of several candidate models; we generate, via stochastic simulation, a huge amount of artificial time series both density‐independent and dependent, with and without exogenous covariates, using different dataset sizes, noise levels and parameter values. Our findings show that SRM outperforms traditional ICs, because generally a) it recognizes the model underlying the data with higher frequency, and b) it leads to lower errors in out‐of‐samples predictions. SRM superiority is specially apparent with short time series. We finally apply SRM to the population records of Alpine ibex Capra ibex living in the Gran Paradiso National Park (Italy), already investigated by other authors via traditional statistical methods; we both analyze their models and introduce some novel ones. We show that models that are best according to SRM show also the lowest leave‐one‐out cross‐validation error.