Where do we aspire to publish? A position paper on scientific communication in biochemistry and molecular biology.

The scientific publication landscape is changing quickly, with an enormous increase in options and models. Articles can be published in a complex variety of journals that differ in their presentation format (online-only or in-print), editorial organizations that maintain them (commercial and/or society-based), editorial handling (academic or professional editors), editorial board composition (academic or professional), payment options to cover editorial costs (open access or pay-to-read), indexation, visibility, branding, and other aspects. Additionally, online submissions of non-revised versions of manuscripts prior to seeking publication in a peer-reviewed journal (a practice known as pre-printing) are a growing trend in biological sciences. In this changing landscape, researchers in biochemistry and molecular biology must re-think their priorities in terms of scientific output dissemination. The evaluation processes and institutional funding for scientific publications should also be revised accordingly. This article presents the results of discussions within the Department of Biochemistry, University of São Paulo, on this subject.

Lycopene and beta-carotene protect in vivo iron-induced oxidative stress damage in rat prostate.

It has been suggested that iron overload may be carcinogenic. In the present study, we evaluated the effect of plasma and prostate carotenoid concentration on oxidative DNA damage in 12-week-old Wistar rats treated with intraperitoneal (ip) ferric nitrilotriacetate (Fe-NTA) (10 mg Fe/kg). Plasma beta-carotene and lycopene concentrations were measured as a function of time after ip injection of carotenoids (10 mg kg(-1) day(-1) beta-carotene or lycopene) in rats. The highest total plasma concentration was reached 3 and 6 h after ip injection of lycopene or beta-carotene, respectively. After 5 days of carotenoid treatment, lycopene and beta-carotene were present in the 0.10-0.51 nmol/g wet tissue range in the prostate. Using a sensitive method to detected 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) by HPLC/EC, the level of 8-oxodGuo in rat prostate DNA was significantly higher (6.3 +/- 0.6 residues/10(6) dGuo) 3 h after Fe-NTA injection compared with control rats (1.7 +/- 0.3 residues/10(6) dGuo). Rats supplemented with lycopene or beta-carotene for 5 days prior to Fe-NTA treatment showed a reduction of about 70% in 8-oxodGuo levels to almost control levels. Compared with control rats, the prostate of Fe-NTA-treated animals showed a 78% increase in malondialdehyde accumulation. Lycopene or beta-carotene pre-treatment almost completely prevented lipid damage. Epidemiological studies have suggested a lower risk of prostate cancer in men reporting a higher consumption of tomato products. However, before associating this effect with tomato sauce constituents, more information is required. The results described here may contribute to the understanding of the protective effects of carotenoids against iron-induced oxidative stress.

Singlet oxygen induced single-strand breaks in plasmid pBR322 DNA: the enhancing effect of thiols.

The biologically occurring thiols, glutathione, cysteamine and cysteine, significantly enhance the single-strand breaks in plasmid pBR322 DNA induced by singlet molecular oxygen (1O2) generated by the thermodissociation of the endoperoxide of 3,3'-(1,4-naphthylidene)dipropionate. The enhancing effect was also observed with chemically related sulfhydryl compounds but not by disulfides. In contrast, dihydrolipoate and its disulfide lipoate protected the plasmid DNA. Metal chelators as well as superoxide dismutase or catalase had no effect, whereas mannitol or sodium azide, decreased the thiol-1O2-induced strand breaks. It is concluded that the observed effects are mediated by reactive oxidation products arising from the 1O2-oxidation of thiols.

5-Aminolevulinic acid induces single-strand breaks in plasmid pBR322 DNA in the presence of Fe2+ ions.

5-Aminolevulinic acid (ALA), a heme precursor accumulated in chemical and inborn porphyrias, has been demonstrated to produce reactive oxygen species upon metal-catalyzed aerobic oxidation and to cause oxidative damage to proteins, liposomes and subcellular structures. Exposure of plasmid pBR322 DNA to ALA (0.01-3 mM) in the presence of 10 microM Fe2+ ions causes DNA single-strand breaks (ssb), revealed by agarose gel electrophoresis as an increase in the proportion of the open circular form (75 +/- 7.5% at 3 mM ALA) at the expense of the supercoiled form. Addition of either anti-oxidant enzymes such as superoxide dismutase (10 micrograms/ml) and catalase (20 micrograms/ml), or a metal chelator (DTPA, 2.5 mM), or a HO. scavenger (mannitol, 100 mM) inhibited the damage (by 30, 45, 55, and 81%, respectively), evidencing the involvement of O2-., H2O2 and HO. (by the Haber-Weiss reaction) in this process. Hydrogen peroxide (100 microM) or Fe2+ (10 microM) alone were of little effect on the extent of DNA ssb. The present data may shed light on the correlation reported between primary liver-cell carcinoma and intermittent acute porphyria.

Singlet molecular oxygen causes loss of biological activity in plasmid and bacteriophage DNA and induces single-strand breaks.

Damage of plasmid and bacteriophage DNA inflicted by singlet molecular oxygen (1O2) includes loss of the biological activity measured as transforming capacity in E. coli and single-strand break formation. Three different sources of 1O2 were employed: (i) photosensitization with Rose bengal immobilized on a glass plate physically separated from the solution; (ii) thermal decomposition of the water-soluble endoperoxide 3,3'-(1,4-naphthylidene) dipropionate (NDPO2); and (iii) microwave discharge. Loss of transforming activity was documented after exposing bacteriophage M13 DNA to 1O2 generated by photosensitization employing immobilized Rose bengal, and with bacteriophage luminal diameter X174 DNA, using the thermodissociable endoperoxide (NDPO2) as a source of 1O2. These findings are in agreement with experiments in which plasmid DNA pBR322 was exposed to a gas stream of 1O2 generated by microwave discharge. The effects of 1O2 quenchers and of 2H2O indicate 1O2 to be the species responsible. Strand-break formation in pBR322 and luminal diameter X174, measured as an increase of the open circular form at the expense of the closed circular supercoiled form, was observed without alkaline treatment after exposing the DNA to 1O2, using either agarose gel electrophoresis or sucrose gradient separation. The effect of quenchers and 2H2O indicate the involvement of 1O2 in DNA damage. We conclude that singlet oxygen can cause loss of biological activity and DNA strand breakage.

Are dioxetanes chemiluminescent intermediates in lipoperoxidation?

Ultraweak chemiluminescence arising from lipoperoxidation has been attributed by several authors to the radiative deactivation of singlet oxygen and triplet carbonyl products. The latter emitters have been suggested to come from annihilation of RO. and ROO. radicals as well as from the thermolysis of dioxetane intermediates formed by (2 + 2) cycloaddition of 1O2 to polyunsaturated fatty acids. This article questions possible dioxetane intermediacy in lipoperoxidation, as the literature clearly states that addition of 1O2 to alpha-hydrogen-containing alyphatic olefins yields only the corresponding allylic hydroperoxides. These compounds may undergo dark thermal or Lewis acid-assisted decomposition to the same product obtained from dioxetane cleavage. Here, reexamining the chemiluminescence properties of dioxygenated tetramethylethylene and linoleic acid and comparing them with those of tetraethyldioxetane, a hindered dioxetane, we corroborate the literature information that only steric hindrance leads to dioxetane formation upon singlet oxygen addition to electron-poor olefins, albeit in very low yields. Proton nuclear magnetic resonance (1H-NMR) analysis, quenching by dioxygen and energy transfer studies to 9,10-dibromoanthracene, as well as gas chromatography (GC) analysis of triphenylphosphine-treated and untreated photo- and chemically dioxygenated olefins support our final conclusion that dioxetane formation during lipoperoxidation can be safely excluded on the basis of the data presently available.

Singlet molecular oxygen production in the reaction of peroxynitrite with hydrogen peroxide.

Peroxynitrite and hydrogen peroxide are mediators of cytotoxicity. This study shows that the peroxynitrite anion reacts with hydrogen peroxide to release oxygen accompanied by emission of chemiluminescence (CL). Direct characterization of this light emission attributes it to the transition of singlet molecular oxygen to the triplet ground state. Chemiluminescence was monitored: (i) by dimol light emission in the red spectral region (> 610 nm) using a red-sensitive photomultiplier; and (ii) by monomol light emission in the infrared (1270 nm) with a liquid nitrogen-cooled germanium diode. These properties of photoemission and the enhancing effect of deuterium oxide on CL intensity as well as the quenching effect of sodium azide are diagnostic of molecular oxygen in the excited singlet state. For comparison, singlet molecular oxygen arising from the thermolysis of the water-soluble endoperoxide of 3,3'-(1,4-naphthylidene)dipropionate or from the hypochlorite/H2O2 system was also monitored. These novel observations identify a potential singlet oxygen-dependent mechanism contributing to cytotoxicity mediated by peroxynitrite and hydrogen peroxide.

Hydroxyl radicals are involved in the oxidation of isolated and cellular DNA bases by 5-aminolevulinic acid.

5-Aminolevulinic acid (ALA) is a heme precursor, pathological accumulation of which is associated with liver cancer. We show that the reactive oxygen species produced upon ALA metal-catalyzed oxidation promote the formation of several radical-induced base degradation products in isolated DNA. The distribution of modified bases is similar to that obtained upon gamma irradiation. This observation strongly suggests the involvement of hydroxyl radicals in the ALA-mediated DNA damage. Increased levels of 8-oxo-7,8-dihydro-2'-deoxyguanosine and 5-hydroxy-2'-deoxycytidine in organ DNA of rats chronically treated with ALA were observed. This is strongly suggestive of the implication of hydroxyl radicals in the ALA-induced degradation of cellular DNA.

Antioxidant defense systems: the role of carotenoids, tocopherols, and thiols.

Reactive oxygen species occur in tissues and can damage DNA, proteins, carbohydrates, and lipids. These potentially deleterious reactions are controlled by a system of enzymatic and nonenzymatic antioxidants which eliminate prooxidants and scavenge free radicals. The ability of the lipid-soluble carotenoids to quench singlet molecular oxygen may explain some anticancer properties of the carotenoids, independent of their provitamin A activity. Tocopherols are the most abundant and efficient scavengers of hydroperoxyl radicals in biological membranes. Water-soluble antioxidants include ascorbate and cellular thiols. Glutathione is an important substrate for enzymatic antioxidant functions and is capable of nonenzymatic radical scavenging. Thiols associated with membrane proteins may also be important to the antioxidant systems. Interactions between the thiols, tocopherols, and other compounds enhance the effectiveness of cellular antioxidant defense.

Singlet oxygen induces predominantly G to T transversions on a single-stranded shuttle vector replicated in monkey cells.

To elucidate the mechanisms of mutagenesis by singlet oxygen DNA damage in mammalian cells, a SV40-derived single-stranded shuttle vector was exposed to the water soluble endoperoxide 3,3'-(1,4-naphthylidene) dipropionate (NDPO2). The damaged vector was transfected into monkey COS7 cells and the plasmid progeny exhibited up to 10 fold increase on the mutation frequency in the supF target gene, when compared to untreated vector. The sequence in the supF locus of such mutants revealed that singlet oxygen-induced mutagenesis in single-stranded vector is significantly different from spontaneous mutagenesis. Among the base substitutions, most of the mutations involved deoxyguanosines, being G to T transversions the predominant type of change. The data indicate that mutagenesis by singlet oxygen in mammalian cells may be generated by an error prone bypass of damaged deoxyguanosines at the template DNA.

Horseradish peroxidase-catalyzed conjugation of eugenol with basic amino acids.

L-Lysine is shown to yield an adduct with the quinone methide intermediate formed during the horseradish peroxidase (HRP)-catalyzed aerobic oxidation of eugenol (4-allyl-2-methoxyphenol). Adduct formation is evidenced by (i) lysine quenching of the characteristic quinone methide absorption band measured at 350 nm; arginine and gamma-aminobutyric acid, but not alanine or propionic acid showed similar behaviour (ii) lysine-promoted a 400 mV decrease of the eugenol oxidation voltammetric wave (1.00 V), concomitantly with an increase in current intensity and (iii) reverse phase HPLC isolation of the lysine eugenol adduct, followed by GC-MS analysis. The MS spectrum is consistent with a 2:1 lysine:eugenol adduct (MW = 455). If operative in vivo, binding of lysine to eugenol might lead to protein inactivation and possibly be involved in eugenol toxicity.

Visible chemiluminescence associated with the reaction between methemoglobin or oxyhemoglobin with hydrogen peroxide.

Visible chemiluminescence is emitted in the irreversible deactivation of hemoglobin or methemoglobin with excess H2O2. The emission takes place in two phases. The most intense one lasts a few seconds and is followed by a second phase of lower intensity that remains for longer periods. This second phase presents chaotic or sustained oscillations. Free radicals are implicated in the luminescent process since the emission can be reduced by free radical scavengers such as 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid (Trolox) or ascorbic acid. These additives lead to a delay in reaching the maximum intensity, which can be related to their consumption, implying substantial recycling of the hemoprotein. Chemiluminescence is also observed in the oxidation of hemin by H2O2, suggesting a role for the heme group in the processes leading to the excited state production. The lower intensity observed in the presence of hemin can be related to the contribution of the globin chains.

Singlet oxygen induced DNA damage and mutagenicity in a single-stranded SV40-based shuttle vector.

The effects of singlet oxygen (1O2), generated by the thermal decomposition of water soluble NDPO2 (endoperoxide of the disodium 3,3'-(1,4-naphthylidene) dipropionate), on a single-stranded shuttle vector were analysed. 1O2 induces a much higher level of breaks in the phosphodiester backbone of single-stranded than double-stranded DNA. This may be due to a higher accessibility of guanine residue, primarily damaged by 1O2. The damaged vector was transfected into monkey COS7 cells where single-stranded DNA was converted to the double-stranded replicative form DNA. After 3 days, extrachromosomal DNA was extracted and the plasmids rescued in E. coli to study mutagenesis. There is a significant increase in mutation frequency of damaged single-stranded DNA in comparison to untreated DNA. It is concluded that 1O2 induces breaks in the backbone of single-stranded DNA and that the 1O2-damaged molecules are mutated after passage through mammalian cells.

Mutation spectrum induced by singlet oxygen in Escherichia coli deficient in exonuclease III.

The repair of singlet oxygen (1O2)-induced DNA lesions requires several enzymes of the nucleotide and base excision repair pathways, including exonuclease III and endonuclease IV that are known apurinic/apyrimidinic-endonucleases in Escherichia coli. In order to better understand the relevance of exonuclease III on the repair of these lesions, we investigated the mutagenic events that result from the replication of a 1O2-damaged plasmid in an exonuclease-deficient host (xth). The mutation spectrum in the tRNA supF gene target indicated that the absence of exonuclease III does not change the types of mutations induced by 1O2 (mostly of G:C-->T:A and G:C-->C:G transversions). However, the spectrum shows that the mutations are scattered in the supF gene, which is significatively different from the one obtained in wild-type bacteria. Thus, exonuclease III may act on the repair of 1O2-induced lesions altering the DNA repair sequence specificity.

Singlet molecular oxygen induced mutagenicity in a mammalian SV40-based shuttle vector.

We have determined the deleterious effects of singlet oxygen (1O2), generated by thermal decomposition of the water-soluble endoperoxide 3,3'-(1,4-naphthylidene)dipropionate (NDPO2), on plasmid DNA. By following the electrophoretic mobility of DNA on agarose gels, we detected single and double strand breaks induced by treatment with NDPO2. The vector employed was a mammalian shuttle vector and the mutagenic consequences of these damages were investigated, using as mutation target the supF suppressor tRNA gene. A high increase of the mutation frequency, over the background, was observed in plasmids transfected in bacteria or after passage through mammalian cells. Trapping agents and quencher effects and other controls confirm the involvement of 1O2 in DNA damage and mutagenicity. These findings indicate that 1O2 can induce DNA lesions which are repaired by an error-prone process in prokaryotic and eukaryotic cells.

Peroxidase activity may play a role in the cytotoxic effect of indole acetic acid.

Peroxidase activity in neutrophils is higher than in thioglycollate macrophages, while in lymphocytes this enzyme activity is very low. Indole-3-acetic acid is oxidized by peroxidase and the role of this enzyme in the cytotoxic effect of the compound was evaluated by measuring oxygen consumption, light emission and cell death in neutrophils, macrophages and lymphocytes. The increase in light emission, oxygen consumption and rate of cell death in cells cultured in the presence of indole-3-acetic acid presented a direct correlation with the peroxidase activity of the cells as follows: neutrophils > thioglycollate macrophages > resident macrophages > lymphocytes. Indeed, in lymphocytes that possess very low peroxidase activity, indole-3-acetic acid did not result in an increase in light emission or oxygen consumption and it was not cytotoxic.

Supramolecular cationic tetraruthenated porphyrin induces single-strand breaks and 8-oxo-7,8-dihydro-2'-deoxyguanosine formation in DNA in the presence of light.

The aim of this investigation is the evaluation of DNA interaction of with tetraruthenated porphyrin (TRP) and of DNA damage in the presence of light. Direct-fluorescence and electronic absorption measurements after incubation of DNA with TRP indicate strong binding between pBR322 DNA or calf thymus DNA with the modified porphyrin. Exposure of pBR322 DNA to TRP (up to 3 microM) and light leads to single-strand break formation as determined by the conversion of the supercoiled form (form I) of the plasmid into the nicked circular form (form II). Oxidative DNA base damage was evaluated by the detection of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) after irradiation of calf thymus DNA in the presence of the TRP. The data demonstrated a dose and time dependence with each type of DNA damage. These data indicate (1) a specificity of the binding mode and (2) type I and II photoinduced mechanisms leading to strand scission activity and 8-oxodGuo formation. Accordingly, singlet molecular oxygen formation, after TRP excitation, was confirmed by near-infrared emission. From these investigations a potential application of TRP in photodynamic therapy is proposed.

Zinc tetraruthenated porphyrin binding and photoinduced oxidation of calf-thymus DNA.

The photooxidation of calf-thymus DNA has been investigated in the presence of a supramolecular tetraruthenated zincporphyrin (ZnTRP) sensitizer. A strong interaction of ZnTRP with DNA has been observed, exhibiting a gradual transition from a non-specific electrostatic binding mode to a more specific one at high DNA concentrations. Formation of O2(1delta(g)) has been detected from its near-infrared emission, after the excitation of ZnTRP in dioxygen-containing solutions. In the presence of DNA and dioxygen, ZnTRP promotes efficient photocatalytic oxidation of the 2'-deoxyguanosine sites, via their direct reaction with O2(1delta(g)), as in a previous work on the ZnTRP-photoinduced oxidation of the free nucleosides.

Activity of thiols as singlet molecular oxygen quenchers.

Singlet molecular oxygen O2(1 delta g) arising from the thermodissociation of the endoperoxide of 3,3'-(1,4-naphthylidene) dipropionate (NDPO2) was used to assess the quenching ability of various thiols and related compounds in sodium phosphate buffer in D2O at 37 degrees C. The overall quenching ability decreases in the sequence ergothioneine, methionine, cysteine, beta,beta-dimethyl cysteine (penicillamine), mercaptopropionylglycine, mesna, glutathione (GSH), dithiothreitol, N-acetyl cysteine and captopril. Cystine, glutathione disulphide, dimesna, methionine sulphone and methionine sulphoxide have no quenching effect. Comparison of the rate constants for physical (kq) with chemical (kr) quenching by thiols indicates that chemical reactivity accounts fully for their ability to quench O2(1 delta g), and pD dependence indicates that the thiolate anion reacts with O2(1 delta g). Loss of thiol groups, as exemplified by GSH, is not affected by the free radical scavengers superoxide dismutase and mannitol. However, sodium azide, a scavenger of O2(1 delta g), completely prevents NDPO2-induced thiol depletion. Depletion of GSH by NDPO2 is accompanied by the formation of its disulphide, sulphinate, sulphonate, sulphoxide and other products.

Ghost protein damage by peroxynitrite and its protection by melatonin.

We have studied the effect of peroxynitrite (ONOO-) on the membrane cytoskeleton of red blood cells and its protection by melatonin. Analysis of the protein fraction of the preparation by SDS-PAGE revealed a dose-dependent (0-600 microM ONOO-) disappearance at pH 7. 4 of the main proteins: spectrin, band 3, and actin, with the concomitant formation of high-molecular weight aggregates resistant to reduction by ss-mercaptoethanol (2%) at room temperature for 20 min. These aggregates were not solubilized by 8 M urea. Incubation of the membrane cytoskeleton with ONOO- was characterized by a marked depletion of free sulfhydryl groups (50% at 250 microM ONOO-). However, a lack of effect of ss-mercaptoethanol suggests that, under our conditions, aggregate formation is not mediated only by sulfhydryl oxidation. The lack of a protective effect of the metal chelator diethylenetriaminepentaacetic acid confirmed that (ONOO-)-induced oxidative damage does not occur only by a transition metal-dependent mechanism. However, we demonstrated a strong protection against cytoskeletal alterations by desferrioxamine, which has been described as a direct scavenger of the protonated form of peroxynitrite. Desferrioxamine (0.5 mM) also inhibited the loss of tryptophan fluorescence observed when the ghosts were treated with ONOO-. Glutathione, cysteine, and Trolox (1 mM), but not mannitol (100 mM), were able to protect the proteins against the effect of ONOO- in a dose-dependent manner. Melatonin (0-1 mM) was especially efficient in reducing the loss of spectrin proteins when treated with ONOO- (90% at 500 microM melatonin). Our findings show that the cytoskeleton, and in particular spectrin, is a sensitive target for ONOO-. Specific antioxidants can protect against such alterations, which could seriously impair cell dynamics and generate morphological changes.