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.

Efeito embriotóxico, teratogênico e abortivo de plantas medicinais / Embryotoxic, teratogenic and abortive effects of medicinal plants

O uso milenar de plantas medicinais mostrou ao longo dos anos, que determinadas plantas apresentam substâncias potencialmente perigosas. Do ponto de vista científico, algumas pesquisas mostraram que muitas dessas plantas possuem substâncias agressivas e por essa razão devem ser utilizadas com cuidado, respeitando seus riscos toxicológicos. Os efeitos mais preocupantes do uso indiscriminado de plantas medicinais são embriotóxico, teratogênico e abortivo, uma vez, que os constituintes da planta podem atravessar a placenta, chegar ao feto e gerar um desses efeitos. Este estudo objetiva fornecer uma listagem das principais plantas medicinais que tenham efeitos embriotóxicos, teratogênicos e abortivos comprovados, conhecendo as partes da planta utilizadas e seus respectivos nomes científicos, com a finalidade de alertar gestantes quanto aos riscos de seu uso. Realizou-se buscas nas bases eletrônicas de dados SciELO, PubMed, MEDLINE, LILACS, CAPES e Google acadêmico. Nos resultados encontrados, plantas como Arnica (Arnica montana), Artemísia (Artemisia vulgaris), Arruda (Ruta chalepensis/ Ruta graveolens), Barbatimão (Stryphnodendron polyphyllum), Boldo (Vernonia condensata) dentre outras, podem vir a gerar um desses efeitos. A partir deste estudo comprova-se que para a maioria das plantas medicinais não há dados a respeito da segurança de seu uso durante a gravidez.

The ancient use of medicinal plants has shown over the years that certain plants have potentially dangerous substances. From a scientific point of view, some studies have shown that many of these plants contain aggressive substances and therefore should be used with caution, respecting their toxicological risks. The most important effects of the indiscriminate use of medicinal plants are embryotoxic, teratogenic and abortifacient since the plant constituents can cross the placenta, reaching the fetus and leading to one of these effects. This study aimed to provide a list of the major medicinal plants that have proven embryotoxic, teratogenic and abortifacient effects, including the used plant parts and their respective scientific names, in order to warn pregnant women about the risks of its use. Searches were carried out in the electronic databases SciELO, PubMed, MEDLINE, LILACS, CAPES and Google Scholar. Results indicated that plants such as mountain arnica (Arnica montana), mugwort (Artemisia vulgaris), fringed rue (Ruta chalepensis / Ruta graveolens), "Barbatimão" (Stryphnodendron polyphyllum) and "Boldo" (Vernonia condensata) are likely to generate such an effect. This study shows that for most medicinal plants there are not data regarding the safety of their use during pregnancy.

SpotWhatR: a user-friendly microarray data analysis system

SpotWhatR is a user-friendly microarray data analysis tool that runs under a widely and freely available R statistical language (http://www.r-project.org) for Windows and Linux operational systems. The aim of SpotWhatR is to help the researcher to analyze microarray data by providing basic tools for data visualization, normalization, determination of differentially expressed genes, summarization by Gene Ontology terms, and clustering analysis. SpotWhatR allows researchers who are not familiar with computational programming to choose the most suitable analysis for their microarray dataset. Along with well-known procedures used in microarray data analysis, we have introduced a stand-alone implementation of the HTself method, especially designed to find differentially expressed genes in low-replication contexts. This approach is more compatible with our local reality than the usual statistical methods. We provide several examples derived from the Blastocladiella emersonii and Xylella fastidiosa Microarray Projects. SpotWhatR is freely available at http://blasto.iq.usp.br/~tkoide/SpotWhatR, in English and Portuguese versions. In addition, the user can choose between [quot ]single experiment[quot ] and [quot ]batch processing[quot ] versions.

Particulate bone grafting of osteolytic femoral lesions around stable cementless stems.

The purpose of the current study was to evaluate the effect of particulate grafting for proximal femoral osteolysis in the presence of a well-fixed cementless femoral stem at the time of acetabular liner change or revision. Sixteen patients (17 hips) who averaged 51 years of age underwent curettage and packing of proximal femoral osteolytic lesions with cancellous allograft. Modular acetabular liners were changed in 11 patients, acetabular revisions were performed in six patients, and femoral heads were exchanged in all patients. The femoral component was retained in all patients. The majority of patients were asymptomatic before revision surgery. The size of the femoral osteolytic lesions was measured preoperatively and postoperatively with anteroposterior and Lauenstein lateral radiographs of the hip. Preoperatively, the average lesion was 41 x 16 mm on the anteroposterior view and 18 x 7 mm on the lateral view. The average clinical and radiographic followup was 39 and 32 months, respectively, with a minimum followup of 24 months. All but one patient remained asymptomatic during the followup period and no femoral stem showed evidence of loosening. The size of the femoral osteolytic lesion averaged 16 x 6 mm on the anteroposterior view and 6 x 2 mm on the lateral view at most recent followup. In 15 of 17 patients, the size of the femoral lesion had regressed. This technique seems to be a viable means of preventing progressive osteolysis and femoral loosening while preserving bone stock for future reconstruction.

The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis.

Xylella fastidiosa is a fastidious, xylem-limited bacterium that causes a range of economically important plant diseases. Here we report the complete genome sequence of X. fastidiosa clone 9a5c, which causes citrus variegated chlorosis--a serious disease of orange trees. The genome comprises a 52.7% GC-rich 2,679,305-base-pair (bp) circular chromosome and two plasmids of 51,158 bp and 1,285 bp. We can assign putative functions to 47% of the 2,904 predicted coding regions. Efficient metabolic functions are predicted, with sugars as the principal energy and carbon source, supporting existence in the nutrient-poor xylem sap. The mechanisms associated with pathogenicity and virulence involve toxins, antibiotics and ion sequestration systems, as well as bacterium-bacterium and bacterium-host interactions mediated by a range of proteins. Orthologues of some of these proteins have only been identified in animal and human pathogens; their presence in X. fastidiosa indicates that the molecular basis for bacterial pathogenicity is both conserved and independent of host. At least 83 genes are bacteriophage-derived and include virulence-associated genes from other bacteria, providing direct evidence of phage-mediated horizontal gene transfer.

PEST sequences in cAMP-dependent protein kinase subunits of the aquatic fungus Blastocladiella emersonii are necessary for in vitro degradation by endogenous proteases.

During Blastocladiella emersonii germination, the regulatory (R) and the catalytic (C) subunits of the cAMP-dependent protein kinase (PKA) are rapidly and concurrently degraded, after PKA activation in response to a transient increase in intracellular cAMP levels. The possibility that PEST sequences could be acting as proteolytic recognition signals in this process was investigated, and high score PEST sequences were found in both B. emersonii R and C subunits. Deletions in the PEST sequences were obtained by site-directed mutagenesis and the different PKA subunits were independently expressed in Escherichia coli. Proteolysis assays of the various R and C recombinant forms, using B. emersonii cell extracts as the source of proteases, showed a strong correlation between the presence of high score PEST sequences and susceptibility to degradation. Furthermore, the amino-terminal sequence of the proteolytic fragments indicated that the cleavage sites in both subunits are located at or near the PEST regions. The PEST sequence in B. emersonii C subunit, which when deleted or disrupted leads to resistance to proteolysis, is entirely contained in the 72-amino-acid extension located in the N-terminus of the protein. C subunit mutants carrying deletions in this region displayed little difference in their kinetic properties or enzyme thermostability. These results suggest that the N-terminal extension may only play a role in C subunit degradation.

Characterization and submitochondrial localization of the alpha subunit of the mitochondrial processing peptidase from the aquatic fungus Blastocladiella emersonii.

In an effort to investigate the molecular mechanisms responsible for the drastic morphological changes the mitochondria go through during the life cycle of the aquatic fungus Blastocladiella emersonii, the gene encoding the alpha subunit of the mitochondrial processing peptidase (alpha-MPP) was isolated. Nucleotide sequence analysis revealed that the predicted alpha-MPP polypeptide comprises 474 amino acids with a calculated molecular mass of 51,900 Da, presenting a characteristic mitochondrial signal sequence. Northern blot analysis indicated a single 1.4-kb transcript encoding the B. emersonii alpha-MPP, whose levels decrease during sporulation, becoming very low in the zoospore, and increase again during germination. Despite these variations in mRNA concentration, B. emersonii alpha-MPP protein levels do not change significantly during the life cycle of the fungus, as observed in Western blots. Experiments to investigate the submitochondrial localization of B. emersonii alpha-MPP and beta-MPP were also carried out, and the results indicated that both subunits are associated with the mitochondrial inner membrane, possibly as part of the bc1 complex, as described for plants.

A P-type ATPase from the aquatic fungus Blastocladiella emersonii similar to animal Na,K-ATPases.

We have cloned a P-type ATPase gene from the aquatic fungus Blastocladiella emersonii (BePAT1) using a probe obtained with degenerate oligonucleotides, corresponding to two amino acid sequences highly conserved among all P-type ATPase isoforms, and the polymerase chain reaction technique. Nucleotide sequence analysis revealed a 3.4 kb open reading frame encoding a putative peptide of 1080 amino acid residues with a calculated molecular mass of 119 kDa, which presents all diagnostic features of P-type transporting ATPases. Comparison to other members of the family and phylogenetic analyses have shown that the BePAT1 protein belongs to the subfamily of Na,K- and H,K-ATPases, indicating that the divergence between the alpha-subunit of the Na,K-ATPase and other members of the P-type ATPase family has occurred before the divergence between the animal and fungal lineages in evolution.

Protein factors in Blastocladiella emersonii cell extracts recognize similar sequence elements in the promoters of the genes encoding cAMP-dependent protein kinase subunits.

Blastocladiella emersonii contains a single cAMP-dependent protein kinase (PKA), which is similar to the mammalian type II isoforms. Its activity is regulated during development by changes in the levels of the catalytic (C) and regulatory (R) subunits, which occur in parallel with changes in levels of the corresponding mRNAs, suggesting coordinate transcriptional control of the expression of both subunits. Both R and C mRNA levels are low in vegetative cells, rise sharply during sporulation and decrease to basal levels again after germination. To investigate sequence elements common to both Blastocladiella R and C gene promoters, which might be involved in the coordinate regulation of these genes, their 5'-flanking regions were analyzed by gel mobility shift and DNase I footprinting assays. We determined that different DNA-protein complexes are generated when fragments of the R and C gene promoters are incubated with extracts from cells expressing (sporulating cells) or not expressing (vegetative cells) both subunits, and competition experiments suggested that similar protein factors bind to both promoters. DNase I footprinting experiments have indicated that a sequence common to both R and C promoters, and similar to mammalian E-boxes, binds factors present in extracts from vegetative and sporulating cells, whereas sequences flanking the E-boxes in both promoters showed a change in the pattern of DNase I digestion only when the vegetative cell extract was used. This result suggests that the composition of the protein complexes binding to these regions changes during sporulation.

Cloning and characterization of the gene for the catalytic subunit of cAMP-dependent protein kinase in the aquatic fungus Blastocladiella emersonii.

We have isolated and characterized cDNA and genomic DNA clones encoding the catalytic subunit (C) of cAMP-dependent protein kinase in the aquatic fungus Blastocladiella emersonii. The C-subunit amino acid sequence derived from the nucleotide sequence predicts a basic polypeptide of 424 residues, excluding the initiator methionine, which by amino-terminal sequence analysis has been shown to be absent from the mature protein. The Blastocladiella C presents a 70-amino-acid extension at the amino terminus, when aligned to the mouse C alpha subunit, being one of the largest C subunits already characterized. The B. emersonii C-gene-coding region is interrupted by three introns, ranging in size over 57-69 bp. The positions of the introns are quite different from those found in other species, suggesting a considerable amount of evolutionary drift in the gene structure. The 5'-flanking region lacks recognizable TATA or CCAAT sequences, is remarkably high in GC content (70%), and primer extension experiments indicate that transcription initiates from multiple sites. Several sequence motifs were identified in the promoter region which could be involved in the developmental control of this gene.

Coordinate pretranslational control of cAMP-dependent protein kinase subunit expression during development in the water mold Blastocladiella emersonii.

The aquatic fungus Blastocladiella emersonii provides a system for studying the regulation of expression of regulatory (R) and catalytic (C) subunits of cAMP-dependent protein kinase (PKA). Blastocladiella cells contain a single PKA with properties very similar to type II kinases of mammalian tissues. During development cAMP-dependent protein kinase activity and its associated cAMP-binding activity change drastically. We have previously shown that the increase in cAMP-binding activity during sporulation is due to de novo synthesis of R subunit and to an increase in the translatable mRNA coding for R (Marques et al., Eur. J. Biochem. 178, 803, 1989). In the present work we have continued these studies to investigate the mechanism by which the changes in the level of kinase activity take place. The C subunit of Blastocladiella has been purified; antiserum has been raised against it and used to determine amounts of C subunit throughout the fungus' life cycle. A sharp increase in C subunit content occurs during sporulation and peaks at the zoospore stage. Northern blot analyses, using Blastocladiella C and R cDNA probes, have shown that the levels of C and R mRNAs parallel their intracellular protein concentrations. These results indicate a coordinate pretranslational control for C and R subunit expression during differentiation in Blastocladiella.

Phosphorylation of ribosomal protein S6 is dependent on cyclic AMP in Dictyostelium discoideum.

Extracts of aggregation-competent cells of Dictyostelium discoideum have an S6 protein kinase activity which is inhibited in the presence of the inhibitor of the cAMP-dependent protein kinase. The phosphorylation of S6 is rapid, and decays rapidly. The S6 kinase activity is detectable in the 150,000g supernatant only in the presence of phosphatase inhibitors known for preserving the S6 kinase in other systems, indicating that the activated form of the enzyme is phosphorylated by the cAMP-dependent protein kinase. S6 kinase elutes as a peak from DEAE-Sephacel at 100 mM NaC1, with an activity that is cAMP-dependent.

Differential expression of heat-shock proteins and spontaneous synthesis of HSP70 during the life cycle of Blastocladiella emersonii.

The heat-shock response in Blastocladiella emersonii is dependent on the developmental stage. Cells exposed to elevated temperatures at different stages of the life cycle (sporulation, germination or growth) show a differential synthesis of heat-shock proteins (hsps). Of a total of 22 polypeptides induced, particular subsets of hsps appear in each phase, demonstrating a non-coordinate heat-shock gene expression. In contrast, heat-shock-related proteins (hsp76, hsp70, hsp39a) are spontaneously expressed at a high level during sporulation. By the criteria of two-dimensional gel electrophoresis and partial proteolysis mapping, the 70,000-Da protein, whose synthesis is induced spontaneously during sporulation, is indistinguishable from the heat-inducible hsp70. The techniques of in vitro translation, and Northern analysis using a Drosophila hsp70 probe, demonstrated that enhanced synthesis of hsp70, which occurs during heat-shock treatment and spontaneously during sporulation, is associated with an accumulation of hsp70 mRNA. These observations suggest that hsp70 gene expression is induced during sporulation.

Heat shock protein synthesis during development in Caulobacter crescentus.

Caulobacter crescentus cells respond to a sudden increase in temperature by transiently inducing the synthesis of several polypeptides. Two of the proteins induced, Hsp62 and Hsp70, were shown to be analogous to the heat shock proteins of Escherichia coli, GroEL and DnaK, respectively, by immunological cross-reactivity with antibodies raised against the E. coli proteins. Two-dimensional gel electrophoretic resolution of extracts of cells labeled with [35S]methionine during heat shock led to the identification of 20 distinct Hsps in C. crescentus which are coordinately expressed, in response to heat, at the various stages of the cell division cycle. Thus, a developmental control does not seem to be superimposed on the transient activation of the heat shock genes. Nonetheless, under normal temperature conditions, four Hsps (Hsp70, Hsp62, Hsp24b, and Hsp23a) were shown to be synthesized, and their synthesis was cell cycle regulated.

Fibrilação ventricular durante teste ergométrico em jovem portadora de prolapso da valva mitral. Relato de caso / Ventricular fibrillation during ergometric test in a young woman with mitral valve prolapse. Report of a case

Uma paciente jovem, portadora da sindrome de prolapso da valva mitral (SPVM), com historia de sincopes desencadeadas por esforco fisico, durante a realizacao do teste ergometrico, apresentou episodio de fibrilacao ventricular, revertida apos cardioversao eletrica. O exame fisico nao revelou dados auscutatorios compativeis com SPVM. O diagnostico foi feito retrospectivamente, atraves do ecocardiograma e do cateterismo cardiaco, caracterizando assim o chamado "prolapso silencioso"

Methylation involved in chemotaxis is regulated during Caulobacter differentiation.

Caulobacter crescentus carries a flagellum and is motile only during a limited time in its cell cycle. We have asked if the biochemical machinery that mediates chemotaxis exists coincident with the cell's structural ability to respond to a chemotactic signal. We first demonstrated that one function of the chemotaxis machinery, the ability to methylate the carboxyl side chains of a specific set of membrane proteins (methyl-accepting chemotaxis proteins, MCPs), is present in C. crescentus. This conclusion is based on the observations that (i) methionine auxotrophs starved of methionine can swim only in the forward direction (comparable to smooth swimming in the enteric bacteria), (ii) a specific set of membrane proteins was found to be methylated in vivo and the incorporated [3H]methyl groups were alkali sensitive, (iii) this same set of membrane proteins incorporated methyl groups from S-adenosylmethionine in vitro, and (iv) out of a total of eight generally nonchemotactic mutants, two were found to swim only in a forward direction and one of these lacked methyltransferase activity. Analysis of in vivo and in vitro methylation in synchronized cultures showed that the methylation reaction is lost when the flagellated swarmer cell differentiates into a stalked cell. In vivo methylation reappeared coincident with the biogenesis of the flagellum just prior to cell division. In vitro reconstitution experiments with heterologous cell fractions from different cell types showed that swarmer cells contain methyltransferase and their membranes can be methylated. However, newly differentiated stalked cells lack methyltransferase activity and membranes from these cells cannot accept methyl groups. These results demonstrate that MCP methylation is confined to that portion of the cell cycle when flagella are present.

Autophosphorylation and rapid dephosphorylation of the cAMP-dependent protein kinase from Blastocladiella emersonii zoospores.

The photoaffinity label 8-azido[32P]adenosine 3':5'-monophosphate and affinity chromatography on N6-(2-aminoethyl)-cAMP-Sepharose were used to analyze the cAMP-binding proteins present in cell-free extracts of Blastocladiella emersonii zoospores. In the presence of a mixture of protease inhibitors, 8-azido[32P]cAMP was specifically and quantitatively incorporated into a major protein band of Mr = 58,000, and three minor protein bands of Mr = 50,000, Mr = 43,000, and Mr = 36,000 respectively, after autoradiography following sodium dodecyl sulfate-polyacryl-amide gel electrophoresis. In the absence of the protease inhibitors, the Mr = 58,000 protein band was converted into the lower molecular weight cAMP-binding proteins, indicating a high sensitivity of the intact Mr = 58,000 protein band to endogenous proteases. The Mr = 58,000 protein corresponded to the regulatory subunit (R), of the cAMP-dependent protein kinase of zoospores, as shown by their identical behavior on DEAE-cellulose chromatography. The partially purified protein kinase incorporated 32P from [gamma-32P] ATP . Mg2+ into R as demonstrated by the specific adsorption of the 32P-labeled protein with N6-(2-aminoethyl)-cAMP-Sepharose. The incorporated 32P group was rapidly removed by endogenous phosphoprotein phosphatases in the presence of cAMP, as shown by pulse-chase experiments with [gamma-32P]ATP. Dephosphorylation of R-cAMP and rapid proteolysis may indicate two other mechanisms, in addition to cAMP, for the control of this protein kinase in vivo.

Induction of germination in Blastocladiella emersonii by cyclic AMP and inhibitors of cyclic AMP phosphodiesterase.

Since K+-induced germination of Blastocladiella emersonii is accompanied by a rapid decrease of a specific cyclic AMP phosphodiesterase (cAMP PDE) activity and a transient cyclic AMP accumulation, the effects of this compound as well as of some inhibitors of cAMP PDE on the induction of germination were tested. Adenine and caffeine, competitive inhibitors of zoospore cAMP PDE, were able to elicit germination in substitution for K+. Cyclic AMP is a poor inducer, but a synergistic effect was evident when non-effective concentrations of K+ and cyclic AMP were added together to the medium. At the same concentration, cyclic GMP had no effect as compared with cyclic AMP. Lanthanum, a specific antagonist of calcium in several biological systems, completely blocked the germination induced by potassium.