What are journals for?

Envisioning the scientific paper of the future

Consider for a moment the rate of advancement in the scientific understanding of DNA. It is formidable; from Fredrich Miescher’s nuclein extraction in the 1860s to Rosalind Franklin’s double helix X-ray in the 1950s to revolutionary next-generation sequencing in the late 2000s. Now consider the scientific paper, the medium used to describe and publish these advances. How is the scientific paper advancing to meet the needs of those who generate and use scientific information? We review four essential qualities for the scientific paper of the future: ( i) a robust source of trustworthy information that remains peer reviewed and is ( ii) communicated to diverse users in diverse ways, ( iii) open access, and ( iv) has a measurable impact beyond Impact Factor. Since its inception, scientific literature has proliferated. We discuss the continuation and expansion of practices already in place including: freely accessible data and analytical code, living research and reviews, changes to peer review to improve representation of under-represented groups, plain language summaries, preprint servers, evidence-informed decision-making, and altmetrics.

How long is too long in contemporary peer review? Perspectives from authors publishing in conservation biology journals

Delays in peer reviewed publication may have consequences for both assessment of scientific prowess in academia as well as communication of important information to the knowledge receptor community. We present an analysis on the perspectives of authors publishing in conservation biology journals regarding their opinions on the importance of speed in peer-review as well as how to improve review times. Authors were invited to take part in an online questionnaire, of which the data was subjected to both qualitative (open coding, categorizing) and quantitative analyses (generalized linear models). We received 637 responses to 6,547 e-mail invitations sent. Peer-review speed was generally perceived as slow, with authors experiencing a typical turnaround time of 14 weeks while their perceived optimal review time was six weeks. Male and younger respondents seem to have higher expectations of review speed than females and older respondents. The majority of participants attributed lengthy review times to reviewer and editor fatigue, while editor persistence and journal prestige were believed to speed up the review process. Negative consequences of lengthy review times were perceived to be greater for early career researchers and to have impact on author morale (e.g. motivation or frustration). Competition among colleagues was also of concern to respondents. Incentivizing peer-review was among the top suggested alterations to the system along with training graduate students in peer-review, increased editorial persistence, and changes to the norms of peer-review such as opening the peer-review process to the public. It is clear that authors surveyed in this study viewed the peer-review system as under stress and we encourage scientists and publishers to push the envelope for new peer-review models.

Minimizing the "re" in review

There is a troubling trend in scientific publishing for manuscripts to undergo multiple, often lengthy, rounds of review, resulting in significant delays to publication. JCB is announcing new procedures to streamline its editorial process and eliminate unnecessary delays.

Evolutionary patterns of carbohydrate transport and metabolism in Halomonas boliviensis as derived from its genome sequence: influences on polyester production

BACKGROUND

Halomonas boliviensis is a halophilic bacterium that is included in the γ-Proteobacteria sub-group, and is able to assimilate different types of carbohydrates. H. boliviensis is also able to produce poly(3-hydroxybutyrate) (PHB) in high yields using glucose as the carbon precursor. Accumulation of PHB by microorganisms is induced by excess of intracellular NADH.The genome sequences and organization in microorganisms should be the result of evolution and adaptation influenced by mutation, gene duplication, horizontal gen transfer (HGT) and recombination. Furthermore, the nearly neutral theory of evolution sustains that genetic modification of DNA could be neutral or selected, albeit most mutations should be at the border between neutrality and selection, i.e. slightly deleterious base substitutions in DNA are followed by a slightly advantageous substitutions.

RESULTS

This article reports the genome sequence of H. boliviensis. The chromosome size of H. boliviensis was 4 119 979 bp, and contained 3 863 genes. A total of 160 genes of H. boliviensis were related to carbohydrate transport and metabolism, and were organized as: 70 genes for metabolism of carbohydrates; 47 genes for ABC transport systems and 43 genes for TRAP-type C4-dicarboxylate transport systems. Protein sequences of H. boliviensis related to carbohydrate transport and metabolism were selected from clusters of orthologous proteins (COGs). Similar proteins derived from the genome sequences of other 41 archaea and 59 bacteria were used as reference. We found that most of the 160 genes in H. boliviensis, c.a. 44%, were obtained from other bacteria by horizontal gene transfer, while 13% of the genes were acquired from haloarchaea and thermophilic archaea, only 34% of the genes evolved among Proteobacteria and the remaining genes encoded proteins that did not cluster with any of the proteins obtained from the reference strains. Furthermore, the diversity of the enzymes derived from these genes led to polymorphism in glycolysis and gluconeogenesis. We found further that an optimum ratio of glucose and sucrose in the culture medium of H. boliviensis favored cell growth and PHB production.

CONCLUSIONS

Results obtained in this article depict that most genetic modifications and enzyme polymorphism in the genome of H. boliviensis were mainly influenced by HGT rather than nearly neutral mutations. Molecular adaptation and evolution experienced by H. boliviensis were also a response to environmental conditions such as the type and amount of carbohydrates in its ecological niche. Consequently, the genome evolution of H. boliviensis showed to be strongly influenced by the type of microorganisms, genetic interaction among microbial species and its environment. Such trend should also be experienced by other prokaryotes. A system for PHB production by H. boliviensis that takes into account the evolutionary adaptation of this bacterium to the assimilation of combinations of carbohydrates suggests the feasibility of a bioprocess economically viable and environmentally friendly.