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.

A rolling-circle miniplasmid of Xanthomonas campestris pv. glycines: the nucleotide sequence and its use as a cloning vector.

The indigenous multicopy miniplasmid (pXG33) of Xanthomonas campestris pv. glycines was entirely sequenced and evaluated as a cloning vector for Xanthomonas. The pXG33 contains 1738 bp and the nucleotide sequence revealed a consensus nicking site (TGATA) described for the pC194 family of rolling-circle replicating (RCR) plasmids. This nicking site is embebbed in a region of high potential to form a number of stem-loop structures. The predicted protein (Rep) showed conserved amino acid residues and potential catalytic regions, containing conserved Tyr and Glu residues. These results indicate that pXG33 replicates by a rolling-circle mechanism. For use as a cloning vector for Xanthomonas, a fragment containing the kanamycin resistance gene (aphA) and the stabilization locus (parB) was inserted into pXG33. The new construct, of 3.4 kb, was designated pXG31. By deletion of the parB locus and using pBluescript KS(+) as an intermediate, pXG40 (2.8 kb), containing unique restriction sites for BamHI, EcoRI, SacI, and KpnI at the ends of the kanamycin resistance gene, was generated. Both constructs showed stability in Xanthomonas during 18 h of growth or 72 h of fermentation, high-copy number, and no interference with pathogenicity. pXG31 and pXG40, however, were incapable of duplication in Escherichia coli and a shuttle vector (pKX33) was constructed by inactivation of some restriction sites of pXG40 and ligation to the cloning vector pBluescript KS(+). pKX33 is nonconjugative, is multicopy, is of low molecular weight (5.7 kb), presents antibiotic resistance markers for ampicillin and kanamycin, has unique restriction sites for KpnI, SalI, EcoRV, EcoRI, BamHI, XbaI, and SacI, and can be used directly for sequencing with universal primers. It can be maintained in E. coli and several species and pathovars of Xanthomonas.

The CIRCE element and its putative repressor control cell cycle expression of the Caulobacter crescentus groESL operon.

The groESL operon is under complex regulation in Caulobacter crescentus. In addition to strong induction after exposure to heat shock, under physiological growth conditions, its expression is subject to cell cycle control. Transcription and translation of the groE genes occur primarily in predivisional cells, with very low levels of expression in stalked cells. The regulatory region of groESL contains both a sigma32-like promoter and a CIRCE element. Overexpression of C. crescentus sigma32 gives rise to higher levels of GroEL and increased levels of the groESL transcript coming from the sigma32-like promoter. Site-directed mutagenesis in CIRCE has indicated a negative role for this cis-acting element in the expression of groESL only at normal growth temperatures, with a minor effect on heat shock induction. Furthermore, groESL-lacZ transcription fusions carrying mutations in CIRCE are no longer cell cycle regulated. Analysis of an hrcA null strain, carrying a disruption in the gene encoding the putative repressor that binds to the CIRCE element, shows constitutive synthesis of GroEL throughout the Caulobacter cell cycle. These results indicate a negative role for the hrcA gene product and the CIRCE element in the temporal control of the groESL operon.