Biochemical and genetic studies on alkaline phosphatase ofCeratitis capitata

Two forms of alkaline phosphatase exist in the integument of the “white pupae” (wp) and dark pupae (dp) mutant strains ofCeratitis capitata, during transition from larvae to pupae. They were separated by DEAE-cellulose chromatography. Both isoenzymes have a molecular weight of approximately 180,000 and two pH optima, at 9.4 and at 11.0. The isoenzymes of the “dark pupae” mutant catalyze the hydrolysis of phosphotyrosine and β-glycerophosphate but not phosphoserine, phosphothreonine, ATP, and AMP. In contrast, the isoenzymes of the white pupae mutant hydrolyze all the substrates tested. The ALPase 1 of the dark pupae mutant was inhibited byL-tyrosine, butL-phenylalanine had no effect on either isoenzyme. The effects of divalent cations, EDTA, temperature, urea, and 2-mercaptoethanol were also investigated. Electrophoretic analysis did not reveal any variants of the larval and pupal isoenzymes, but ALPase A, an adult stage-specific isoenzyme, was found to be polymorphic. The electrophoretic variants were shown to be controlled by three codominant alleles located on the third chromosome ofCeratitis capitata. Since we found no hybrid enzyme, we conclude that ALPase A is monomeric.     

Thyrsiferol Inhibits Mitochondrial Respiration and HIF-1 Activation

The cytotoxic marine red algal metabolite thyrsiferol (1) was found to inhibit hypoxia-induced hypoxia-inducible factor-1 (HIF-1) activation in T47D human breast tumor cells (66% inhibition at 3 μM). Compound 1 also suppressed hypoxic induction of HIF-1 target genes (VEGF, GLUT-1) at the mRNA level, and displayed tumor cell line-selective time-dependent inhibition of cell viability/proliferation. Mechanistic studies revealed that 1 selectively suppressed mitochondrial respiration at Complex I (IC(50) 3 μM). Thyrsiferol represents a prototypical, structurally unique electron transport chain inhibitor. The apparent rotenone-like activity may contribute to the observed cytotoxicity of 1 and play an important role in Laurencia chemical defense.     

Individual‐based and stochastic modeling of cell population dynamics considering substrate dependency

In this article, we propose an individual‐based and stochastic modeling approach that is capable of describing the bacterial cell population dynamics during a batch culture. All stochastic nature inherent in intracellular molecular level reactions and cell division processes were considered in a single model framework by embedding a sub‐model describing individual cell's growth kinetics in a discrete event simulation algorithm. The resultant unique feature of the model is that the effects of the stochasticities on the cell population dynamics can be investigated for different substrate‐dependent cell growth kinetics. When Monod kinetics was used as the sub‐model, the stochasticities only slightly affected the cell mass increase and substrate consumption profiles during the batch culture although they were still important in describing the changes of cell population distributions. When Andrews substrate inhibition kinetics was used, however, it was revealed that the overall cell population dynamics could be seriously influenced by the stochasticities. Under a critical initial substrate level, the cell population could proliferate against the substrate inhibition only when the stochasticities were considered. Biotechnol. Bioeng. 2009;103: 891–899. © 2009 Wiley Periodicals, Inc.     

Knockdown of aquaporin-8 induces mitochondrial dysfunction in 3T3-L1 cells

BackgroundAquaporin-8 (AQP8), a member of the aquaporin water channel family, is expressed in various tissue and cells, including liver, testis, and pancreas. AQP8 appears to have functions on the plasma membrane and/or on the mitochondrial inner membrane. Mitochondrial AQP8 with permeability for water, H₂O₂ and NH₃ has been expected to have important role in various cells, but its information is limited to a few tissues and cells including liver and kidney. In the present study, we found that AQP8 was expressed in the mitochondria in mouse adipose tissues and 3T3-L1 preadipocytes, and investigated its role by suppressing its gene expression.MethodsAQP8-knocked down (shAQP8) cells were established using a vector expressing short hairpin RNA. Cellular localization of AQP8 was examined by western blotting and immunocytochemistry. Mitochondrial function was assessed by measuring mitochondrial membrane potential, oxygen consumption and ATP level measurements.ResultsIn 3T3-L1 cells, AQP8 was expressed in the mitochondria. In shAQP8 cells, mRNA and protein levels of AQP8 were decreased by about 75%. The shAQP8 showed reduced activities of complex IV and ATP synthase; it is probable that the impaired mitochondrial water handling in shAQP8 caused suppression of the electron transport and ADP phosphorylation through inhibition of the two steps which yield water. The reduced activities of the last two steps of oxidative phosphorylation in shAQP8 cause low routine and maximum capacity of respiration and mitochondrial hyperpolarization.ConclusionMitochondrial AQP8 contributes to mitochondrial respiratory function probably through maintenance of water homeostasis.General significanceThe AQP8-knocked down cells we established provides a model system for the studies on the relationships between water homeostasis and mitochondrial function.     

Influence of core histone acetylation on SV40 minichromosome replication in vitro

We have used the SV40 in vitro replication system to analyze the replication efficiencies of SV40 minichromosomes associated with normal or hyperacetylated histones. We found that elongation of replication occurs with higher efficiency in hyperacetylated minichromosomes in comparison with normal minichromosomes. Our results indicate that the movement of the replication machinery through nucleosomal DNA is facilitated by charge neutralization due to acetylation of the histone tails. Edited by: A. Wolffe     

PeroxiBase: the peroxidase database

Peroxidases (EC 1.11.1.x), which are encoded by small or large multigenic families, are involved in several important physiological and developmental processes. Analyzing their evolution and their distribution among various phyla could certainly help to elucidate the mystery of their extremely widespread and diversified presence in almost all living organisms. PeroxiBase was originally created for the exhaustive collection of class III peroxidase sequences from plants (Bakalovic, N., Passardi, F., et al., 2006. PeroxiBase: a class III plant peroxidase database. Phytochemistry 67, 534-539). The extension of the class III peroxidase database to all proteins capable to reduce peroxide molecules appears as a necessity. Our database contains haem and non-haem peroxidase sequences originated from annotated or not correctly annotated sequences deposited in the main repositories such as GenBank or UniProt KnowledgeBase. This new database will allow obtaining a global overview of the evolution the protein families and superfamilies capable of peroxidase reaction. In this rapidly growing field, there is a need for continual updates and corrections of the peroxidase protein sequences. Following the lack of unified nomenclature, we also introduced a unique abbreviation for each different family of peroxidases. This paper thus aims to report the evolution of the PeroxiBase database, which is freely accessible through a web server (http://peroxibase.isb-sib.ch). In addition to new categories of peroxidases, new specific tools have been created to facilitate query, classification and submission of peroxidase sequences.     

Phylogenetic Reconstruction of a Known HIV-1 CRF04_cpx Transmission Network Using Maximum Likelihood and Bayesian Methods

The CRF04_cpx strains of HIV-1 accounts for approximately 2–10% of the infected population in Greece, across different transmission risk groups. CRF04_cpx was the lineage documented in an HIV-1 transmission network in Thessalonica, northern Greece. Most of the transmissions occurred through unprotected heterosexual contacts between 1989 and 1993. Blood samples were available for six patients, obtained 6–10 years later, except for one patient sampled in 1991. Our objective was to examine whether the transmission history is compatible with the evolutionary tree of the virus, in partial gag, partial env, and partial gag+env. The inferred phylogenetic tree obtained using maximum likelihood and Bayesian methods in partial gag+env was much closer to the transmission tree than that using either env or gag separately. Our findings suggest that the epidemiological relationships among patients who have been infected by a common source correspond almost exactly to the evolutionary trees of the virus, given that enough phylogenetic signal is present in the alignment. Moreover, we found evidence that recombination is not the most parsimonious explanation for the phylogenetic incongruence between gag and env. For patients with known infection dates, the estimated dates of the coalescent events obtained using molecular clock calculations based on a newly developed Bayesian method in gag + env were in agreement with the actual infection dates.This article contains online supplementary material.Reviewing Editor: Dr. Lauren Ancel-MeyersIsolated sequences from patients belonging to the CRF04_cpx transmission network always correspond to partially characterized gag, env, and gag+env genomic regions.     

Influence of sequential oligopeptide carriers on the bioactive structure of conjugated epitopes: comparative study of the conformation of a Herpes simplex virus glycoprotein gD-1 epitope in the free and conjugated form, and protein "built-in" crystal structure

Synthetic carriers play an important role in immunogen presentation, due to their ability of inducing improved and specific responses to conjugated epitopes. Their influence on the bioactive conformation of the epitope, though admittedly crucial for relevant in vitro and in vivo applications, is difficult to evaluate, given the usual lack of information on the complex conformational features determined by the nature of the carrier and the mode of ligation. Using the Herpes simplex virus glycoprotein D-1 epitope (Leu(9)-Lys-Nle-Ala-Asp-Pro-Asn-Arg-Phe-Arg-Gly-Lys-Asp-Leu(22)) as a model, we have performed a detailed conformational analysis on the free epitope peptide in solution and on three constructs in which the epitope was conjugated to sequential oligopeptide carriers {Ac-[Lys-Aib-Gly](4)-OH (SOC(4))} (through either a thioether or an amide bond; Ac: acetyl) and polytuftsin oligomers {H-[Thr-Lys-Pro-Lys-Gly](4)-NH(2) (T20)}, (through a thioether bond). The analysis of the epitope conformation in the parent protein, in carrier-conjugated and free form, suggests that the beta-turn structure of the -Asp(13)-Pro-Asn-Arg(16)- segment is highly conserved and independent of the epitope form. However, small conformational variations were observed at the C-terminal part of the epitope, depending on the nature of the carrier.     

Dynamic modelling of high biomass density cultivation and biohydrogen production in different scales of flat plate photobioreactors

This paper investigates the scaling‐up of cyanobacterial biomass cultivation and biohydrogen production from laboratory to industrial scale. Two main aspects are investigated and presented, which to the best of our knowledge have never been addressed, namely the construction of an accurate dynamic model to simulate cyanobacterial photo‐heterotrophic growth and biohydrogen production and the prediction of the maximum biomass and hydrogen production in different scales of photobioreactors. To achieve the current goals, experimental data obtained from a laboratory experimental setup are fitted by a dynamic model. Based on the current model, two key original findings are made in this work. First, it is found that selecting low‐chlorophyll mutants is an efficient way to increase both biomass concentration and hydrogen production particularly in a large scale photobioreactor. Second, the current work proposes that the width of industrial scale photobioreactors should not exceed 0.20 m for biomass cultivation and 0.05 m for biohydrogen production, as severe light attenuation can be induced in the reactor beyond this threshold. Biotechnol. Bioeng. 2015;112: 2429–2438. © 2015 The Authors. Biotechnology and Bioengineering Published by Wiley Peiodicals, Inc.     

C(15) Acetogenins from the red alga Laurencia obtusa.

Four C(15) acetogenins, 13-epilaurencienyne (3Z) (1), 13-epipinnatifidenyne (3E) (2), (3E, 6S(*), 7R(*), 9S(*), 10S(*), 12R(*))-9-chloro-13-bromo-6:12-epoxy-7, 10-diacetoxypentadec-3-en-1-yne (3), (3Z, 6S(*), 7R(*), 9S(*), 10S(*), 12R(*))-9-chloro-13-bromo-6:12-epoxy-7, 10-diacetoxypentadec-3-en-1-yne (4), along with the known 13-epilaurencienyne (3E) (5), have been isolated from the organic extract of the red alga Laurencia obtusa, collected in the Aegean Sea, Greece. The structures of the new natural products, as well as their relative stereochemistry, were established by means of spectral data analysis, including 2D NMR spectroscopic experiments. Some of the new metabolites exhibited significant insecticidal activity.