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.

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.

Lycopene and ß-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 ß-carotene and lycopene concentrations were measured as a function of time after ip injection of carotenoids (10 mg kg-1 day-1 ß-carotene or lycopene) in rats. The highest total plasma concentration was reached 3 and 6 h after ip injection of lycopene or ß-carotene, respectively. After 5 days of carotenoid treatment, lycopene and ß-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 ß-carotene for 5 days prior to Fe-NTA treatment showed a reduction of about 70 percent in 8-oxodGuo levels to almost control levels. Compared with control rats, the prostate of Fe-NTA-treated animals showed a 78 percent increase in malondialdehyde accumulation. Lycopene or ß-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 molecular oxygen triggers the soxRS regulon of Escherichia coli.

The electronically excited molecular oxygen (singlet oxygen, 1O2) can be detrimental to cells in several ways, although recent reports indicate that it may play a role as an intercellular signal in eukaryotes. Here we present evidence that 1O2, generated by thermodissociation of disodium 3,3'-(1,4-naphthylidene) diproprionate endoperoxide, activates transcription of genes of the soxRS regulon, and that this induction is paralleled by induction of a soxS'::lacZ operon fusion. The inductions were dependent on a functional soxR gene. These data imply that protective responses, such as induction of the soxRS regulon, may be triggered by diverse environmental oxidative stresses, and that 1O2 may also function as a signal molecule in prokaryotes.

DNA damage by 3,6-dihydropyrazine-2,5-dipropanoic acid, the cyclic dimerization product of 5-aminolevulinic acid.

5-Aminolevulinic acid (ALA) is a heme precursor that accumulates in lead poisoning and inborn porphyrias. It has been shown to produce reactive oxygen species upon metal-catalyzed aerobic oxidation and to cause oxidative damage to proteins, liposomes, DNA, and subcellular structures. Studies have also shown that ALA may condense to yield the cyclic product 3,6-dihydropyrazine-2,5-dipropanoic acid (DHPY). Here we propose that DHPY could be involved in DNA damage in the presence of high concentrations of ALA. Exposure of plasmid pUC19 DNA to low concentrations of DHPY (2-10 microM) in the presence of 0.1 mM Cu2+ ions causes DNA strand breaks, as demonstrated by agarose gel electrophoresis. It was also shown that in the presence of Cu2+ ions DHPY is able to increase the oxidation of monomeric 2'-deoxyguanosine to form 8-oxo-7,8-dihydro-2'-deoxyguanosine as inferred from high performance liquid chromatography measurements using electrochemical detection. Addition of a metal chelator (bathocuproine, 0.5 mM), the DNA compacting polyamines spermidine (1 mM) and spermine (1 mM) or antioxidant enzymes such as superoxide dismutase (10 microg/ml) and catalase (20 pg/ml) protect the DNA against these damages. The data presented here are discussed with respect to the increased frequency of liver cancer in patients with acute intermittent porphyria.

Singlet oxygen induces oxidation of cellular DNA.

The aim of the present work was to evaluate the potential for (1)O(2) to induce oxidation of cellular DNA. For this purpose cells were incubated in the presence of a water-soluble endoperoxide whose thermal decomposition leads to the formation of singlet oxygen. Thereafter, DNA was extracted and the level of several modified DNA bases was determined by HPLC analysis coupled to a tandem mass spectrometric detection. A significant increase in the level of 8-oxo-7,8-dihydro-2'-deoxyguanosine was observed upon incubation of the cells with the chemical generator of (1)O(2), whereas the level of the other DNA bases measured remained unchanged. To demonstrate that singlet oxygen is directly involved in the formation of 8-oxo-7, 8-dihydro-2'-deoxyguanosine, the corresponding (18)O-labeled endoperoxide was used. Incubation of the cells with such a generator of (18)O-labeled singlet oxygen results in the formation of (18)O-labeled 8-oxo-7,8-dihydro-2'-deoxyguanosine in the nuclear DNA. This result clearly demonstrates that singlet oxygen, when released within cells, is able to directly oxidize cellular DNA.

Protective effect of lycopene on lipid peroxidation and oxidative DNA damage in cell culture.

A high incidence of cancer has been correlated with chronic iron overload, and carotenoids are of interest as possible anticarcinogens. We have investigated the effect of lycopene on lipid peroxidation and on the formation of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) in CV1-P monkey cells exposed to ferric nitrilotriacetate (Fe-NTA) plus ascorbate. Cells supplemented with lycopene (20 pmol/10(6) cells) showed a reduction of 86% in Fe-NTA/ascorbate-induced lipid peroxidation (TBARS). Levels of 8-oxodGuo rose from 1.59+/-0.09 residues/10(6) dGuo in the control cells to 14.02+/-0.41 residues/10(6) dGuo after incubation with (1:4 mM) Fe-NTA/ascorbate (40 microM). Lycopene supplementation decreased in 77% the 8-oxodGuo levels in Fe-NTA/ascorbate-treated cells. These results indicate that lycopene can protect mammalian cells against membrane and DNA damage and possibly play a protective role against tumor promotion associated with oxidative damage.

Singlet oxygen induces oxidation of cellular DNA.

The aim of the present work was to evaluate the potential for (1)O(2) to induce oxidation of cellular DNA. For this purpose cells were incubated in the presence of a water-soluble endoperoxide whose thermal decomposition leads to the formation of singlet oxygen. Thereafter, DNA was extracted and the level of several modified DNA bases was determined by HPLC analysis coupled to a tandem mass spectrometric detection. A significant increase in the level of 8-oxo-7,8-dihydro-2'-deoxyguanosine was observed upon incubation of the cells with the chemical generator of (1)O(2), whereas the level of the other DNA bases measured remained unchanged. To demonstrate that singlet oxygen is directly involved in the formation of 8-oxo-7, 8-dihydro-2'-deoxyguanosine, the corresponding (18)O-labeled endoperoxide was used. Incubation of the cells with such a generator of (18)O-labeled singlet oxygen results in the formation of (18)O-labeled 8-oxo-7,8-dihydro-2'-deoxyguanosine in the nuclear DNA. This result clearly demonstrates that singlet oxygen, when released within cells, is able to directly oxidize cellular DNA.

Peroxynitrite does not decompose to singlet oxygen ((1)Delta (g)O(2)) andnitroxyl (NO(-)).

According to Khan et al. [Khan, A. U., Kovacic, D., Kolbanovskiy, A., Desai, M., Frenkel, K. & Geacintov, N. E. (2000) Proc. Natl. Acad. Sci. USA 97, 2984-2989], peroxynitrite (ONOO(-)) decomposes after protonation to singlet oxygen ((1)Delta(g)O(2)) and singlet oxonitrate (nitroxyl, (1)NO(-)) in high yield. They claimed to have observed nitrosyl hemoglobin from the reaction of NO(-) with methemoglobin; however, contamination with hydrogen peroxide gave rise to ferryl hemoglobin, the spectrum of which was mistakenly assigned to nitrosyl hemoglobin. We have carried out UV-visible and EPR experiments with methemoglobin and hydrogen peroxide-free peroxynitrite and find that no NO(-) is formed. With this peroxynitrite preparation, no light emission from singlet oxygen at 1270 nm is observed, nor is singlet oxygen chemically trapped; however, singlet oxygen was trapped when hydrogen peroxide was also present, as previously described [Di Mascio, P., Bechara, E. J. H., Medeiros, M. H. G., Briviba, K. & Sies, H. (1994) FEBS Lett. 355, 287-289]. Quantum mechanical and thermodynamic calculations show that formation of the postulated intermediate, a cyclic form of peroxynitrous acid (trioxazetidine), and the products (1)NO(-) and (1)Delta(g)O(2) requires Gibbs energies of ca. +415 kJ .mol(-1) and ca. +180 kJ.mol(-1), respectively. Our results show that the results of Khan et al. are best explained by interference from contaminating hydrogen peroxide left from the synthesis of peroxynitrite.

trans,trans-2,4-decadienal-induced 1,N(2)-etheno-2'-deoxyguanosine adduct formation.

A number of ring-extended DNA adducts resulting from the reaction of alpha,beta-unsaturated aldehydes, or their epoxides, with DNA bases have been characterized in recent years. These adducts may lead to miscoding during DNA replication, resulting, if not repaired, in mutations that can contribute to cancer development. trans,trans-2, 4-Decadienal (DDE) is one of the highly cytotoxic aldehydes endogenously formed from lipid peroxidation. To evaluate its DNA damaging potential, we have investigated the reaction of DDE with 2'-deoxyguanosine (dGuo) in the presence of peroxides. Three stable adducts were isolated by reverse-phase HPLC. Adduct A1, 3-(2-deoxy-beta-D-erythro-pentafuranosyl)-5,9-dihydro-9H-imidazo[2 , 1-i]purin-9-hydroxy, is a tautomer of 1, N(2)-etheno-2'-deoxyguanosine, a well-known reaction product of epoxy aldehydes with dGuo. Two new diasteroisomeric products, A2-1 and A2-2, 1-¿[3-(2'-deoxy-beta-D-erythro-pentafuranosyl)-5, 9-dihydro-9H-imidazo[2,1-i]purin-9-hydroxy]-7-yl¿-2-one-3-octanol, were isolated and characterized on the basis of their spectroscopic features as 1,N(2)-etheno adducts possessing a carbon side chain with a carbonyl and a hydroxyl group. The proposed reaction mechanism for the formation of adducts A2 involves DDE double epoxidation and hydrolysis of the C4 epoxy group prior to nucleophilic addition of the exocyclic amino group of dGuo to C1 of the aldehyde, followed by cyclization via nucleophilic attack on the C2 epoxy group by N-1 and elimination of H(2)O. After treatment of calf thymus DNA with DDE, formation of adducts A1 and A2 was detected by the LC/ESI/MS-MS technique. These results can contribute to a better understanding of the chemical structures of adducts resulting from the reaction of aldehydes with nucleic acid bases, a necessary step in assessing the genotoxic risks associated with this class of compounds.

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.

Novel 1,N(6)-etheno-2'-deoxyadenosine adducts from lipid peroxidation products.

trans,trans-2,4-Decadienal (DDE) is a widespread alpha, beta-unsaturated aldehyde found, for example, in food, water, and environmental pollutants. DDE is also endogenously generated as a breakdown product of lipid peroxidation in cell membranes. In the work presented here, the reaction of DDE with 2'-deoxyadenosine (dAdo) was investigated in an effort to assess its possible DNA damage potential. Besides 1,N(6)-etheno-2'-deoxyadenosine and two products, namely, 1-[3-(2-deoxy-beta-D-erythro-pentofuranosyl)-3H-imidazo[2, 1-i]purin-7-yl]-1,2,3-octanetriol (adduct I) and 1-[3-(2-deoxy-beta-D-erythro-pentofuranosyl)-3H-imidazo[2, 1-i]purin-7-yl]-1,2-heptanediol (adduct II), previously described by our group, two novel etheno adducts were identified. Thus, 1-[3-(2-deoxy-beta-D-erythro-pentofuranosyl)-3H-imidazo[2, 1-i]purin-7-yl]-1-hexanol (adduct III) and 1-[3-(2-deoxy-beta-D-erythro-pentofuranosyl)-3H-imidazo[2, 1-i]purin-7-yl]-2,3-epoxy-1-octanol (adduct IV) were isolated by reverse-phase high-performance liquid chromatography and characterized on the basis of extensive spectroscopic measurements. The formation of the adducts is likely to involve initial DDE oxidation followed by generation of reactive intermediates such as diepoxides, epoxides, and/or hydroperoxides. The subsequent reaction of the latter oxidation products with dAdo will give rise to the four described adducts. We also demonstrated here that upon oxidation, DDE reacts with calf thymus DNA, producing the four dAdo adducts. Interestingly, two of them are the expected products arising from the reaction of dAdo with 4-hydroxy-trans-2-nonenal (HNE) and trans-2-octenal, two other important breakdown lipid peroxidation products. The reactivity of DDE with DNA is lower than that of the latter aldehydes. However, DDE produced a wider variety of adducts. The characterization of the different DNA-etheno adducts and the determination of the mechanism of formation are of great importance for a better understanding of the deleterious biological effects associated with this class of compounds.

Peridinin as the major biological carotenoid quencher of singlet oxygen in marine algae Gonyaulax polyedra.

Carotenoids in light-harvesting proteins and reaction centers increase the overall efficiency of photosynthesis by transferring absorbed light energy to chlorophylls. Peridinin and beta-carotene were isolated from Gonyaulax polyedra in a one-step purification protocol using the preparative circular chromatography (Chromatotron), performed on silica gel under N(2) atmosphere and n-hexane/acetone 8:2 as mobile phase and characterized by extensive (1)H NMR, infrared, and electrospray ionization mass spectrometry analyses. The quenching of singlet molecular oxygen [O(2) ((1)Delta(g))] was evaluated by NIR-emission assays using singlet oxygen generated by sensitization of either perinaphthenone or methylene blue. The NIR-emission assay showed that peridinin quench as singlet oxygen (k(q) = 9.5 x 10(8) M(-1) s(-1)) 5-fold less efficiently than beta-carotene (52 x 10(8) M(-1) s(-1)). A method, based on the use of high-performance liquid chromatography with UV-VIS detection, was then developed for the sensitive quantification of peridinin (55% of total carotenoids) and beta-carotene (4.1% of total carotenoids). Thus, since peridinin is 10-fold more abundant than beta-carotene, it is expected to be the major protector against the deleterious effects of O(2) ((1)Delta(g)) in Gonyaulax polyedra.

DNA damage by 5-aminolevulinic and 4,5-dioxovaleric acids in the presence of ferritin.

Cellular accumulation of 5-aminolevulinic acid (ALA), the first specific intermediate of heme biosynthesis, is correlated in liver biopsy samples of acute intermittent porphyria affected patients with an increase in the occurrence of hepatic cancers and the formation of ferritin deposits in hepatocytes. 5-Aminolevulinic acid is able to undergo enolization and to be subsequently oxidized in a reaction catalyzed by iron complexes yielding 4,5-dioxovaleric acid (DOVA). The released superoxide radical (O(*-)(2)) is involved in the formation of reactive hydroxyl radical ((*)OH) or related species arising from a Fenton-type reaction mediated by Fe(II) and Cu(I). This leads to DNA oxidation. The metal catalyzed oxidation of ALA may be exalted by the O(*-)(2) and enoyl radical-mediated release of Fe(II) ions from ferritin. We report here the potentiating effect of ferritin on the ALA-mediated cleavage of plasmid DNA and the enhancement of the formation of 8-oxo-7, 8-dihydro-2'-deoxyguanosine (8-oxodGuo). Plasmid pBR322 was incubated with ALA and varying amounts of purified ferritin. DNA damage was assessed by gel electrophoresis analysis of the open and the linear forms of the plasmid from the native supercoiled structure. Addition of either the DNA compacting polyamine spermidine or the metal chelator ethylenediaminetetraacetic acid (EDTA) inhibited the damage. It was also shown that ALA in the presence of ferritin is able to increase the oxidation of the guanine moiety of monomeric 2'-deoxyguanosine (dGuo) and calf thymus DNA (CTDNA) to form 8-oxodGuo as inferred from high performance liquid chromatography (HPLC) measurements using electrochemical detection. The formation of the adduct dGuo-DOVA was detected in CTDNA upon incubation with ALA and ferritin. In a subsequent investigation, the aldehyde DOVA was also able to induces strand breaks in pBR322 DNA.

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.