Alicia Kowaltowski

Selecting the best journals for our papers

Submitted by redoxoma on Fri, 02/28/2020 - 19:58

Photo by Jacqueline Macou (https://pixabay.com/users/jackmac34-483877/) under Pixabay License

Radical-Free Corner by Alicia Kowaltowski & coauthors ^[1], from Instituto de Química da USP
Corresponding author e-mail: ali-I-am-here-cia@hotmail.com@iq.usp.br

Scientific publications in specialized journals have always been the cornerstone of communication between scientists, allowing for the exchange of new knowledge. However, the number of specialized scientific journals in the Biochemistry and Molecular Biology area has grown quickly within the last few years, and is 50% larger today than it was 15 years ago. Within this changing situation, choosing an adequate journal to submit to requires new considerations. With this in mind, the Department of Biochemistry, University of São Paulo, prepared a published guideline for what it considers should be the main points taken when choosing a journal [1]. The consensus agreement of the 48 authors of this position paper is summarized in the following bullet points:

“-Submit pre-prints whenever possible, avoiding their use only when a target journal does not permit it or it is unadvisable (such as for clinical studies), and then proceed with submission to a quality peer-reviewed journal.

-Value and provide high quality peer-review in scientific journals, both by delivering careful revisions, when requested, and seeking good revisions of submissions.

-Give preference to journals with a solid and time-tested reputation for quality, irrespective of current impact factor.

-Denounce and avoid unfair pricing for both subscription and open access journals.

-Value journals with good visibility, indexed widely, and that appeal to a general audience.

-Give preference to journals with strong links to academic societies and that include active and highly reputable investigators on their boards and advisory committees.”

One much discussed point in 2019 was the idea that scientific publications should be freely accessible to all readers. This concept was pushed strongly by Plan S, an ambitious proposal launched in September 2018 to make open access publications mandatory worldwide by January 2020 (now pushed back to January 2021 [2]). While the Department of Biochemistry authors believe open access publications should prevail in the future, they caution that an uncontrolled and fast push for immediate open access can strengthen two very large problems in the scientific publication landscape: predatory publications [4] and abusive pricing [1].

An alternative that provides immediate open access reading and meets the requirements established in 2019 by our main research funding agency FAPESP [3] is to deposit pre-prints of papers prior to final peer-reviewed publications. Pre-printing is generally recommended by the position paper [1], which also indicates that a final peer-reviewed publication is important for the visibility and quality boost that the revision process provides.

Another point almost universally considered when choosing journals is impact factor. The authors of the position paper caution that impact factors have many caveats, and that the general idea should be to favor a broad audience of scientist readers and not simply a highly flawed number. Instead, the quality of the editorial board, institutions backing the journal (such as reputable scientific societies) and its time-tested reputation should be more important when choosing journals.

Indeed, a collective New Year´s publication resolution [5] should be made among scientists for 2020: to consult the history of a journal and the lists of names in the editorial boards, selecting those with the highest quality scientists in the field, regardless of impact factor. This would ensure the best possible peer-review process for the paper, and therefore contribute toward the generation of high quality Science.

References

M.S. Baptista, M.J.M. Alves, G.M. Arantes, H.A. Armelin, O. Augusto, R.L. Baldini, D.S. Basseres, E.J.H. Bechara, A. Bruni-Cardoso, H. Chaimovich, P. Colepicolo Neto, W. Colli, I.M. Cuccovia, A.M. Da-Silva, P. Di Mascio, S.C. Farah, C. Ferreira, F.L. Forti, R.J. Giordano, S.L. Gomes, F.J. Gueiros Filho, N.C. Hoch, C.T. Hotta, L. Labriola, C. Lameu, M.T. Machini, B. Malnic, S.R. Marana, M.H.G. Medeiros, F.C. Meotti, S. Miyamoto, C.C. Oliveira, N.C. Souza-Pinto, E.M. Reis, G.E. Ronsein, R.K. Salinas, D. Schechtman, S. Schreier, J.C. Setubal, M.C. Sogayar, G.M. Souza, W.R. Terra, D.R. Truzzi, H. Ulrich, S. Verjovski-Almeida, F.V. Winck, B. Zingales, A.J. Kowaltowski. Where do we aspire to publish? A position paper on scientific communication in biochemistry and molecular biology Brazilian Journal of Medical and Biological Research, 52(9): 2019. | doi: 10.1590/1414-431x20198935
E. S. Foundation. 'Plan S' and 'cOAlition S' – Accelerating the transition to full and immediate Open Access to scientific publications [Homepage] 2020. | url: https://www.coalition-s.org
F. Marques. FAPESP lança política para acesso aberto Pesquisa FAPESP [on-line], 2019. | url: https://revistapesquisa.fapesp.br/2019/03/14/fapesp-lanca-politica-para-acesso-aberto/
A. H. P. Duncan. Predatory publishers: the journals that churn out fake science The Guardian [on-line], 2018. | url: https://www.theguardian.com/technology/2018/aug/10/predatory-publishers-the-journals-who-churn-out-fake-science
L. M. Gierasch. JBC’s New Year’s resolutions: Check them off! Journal of Biological Chemistry, 292(52): 21705–6, 2017. | doi: 10.1074/jbc.e117.001461

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A link between mitochondrial shape and function in Ca²⁺ signaling

Submitted by redoxoma on Mon, 09/30/2019 - 13:24

Redoxoma Highlights by Sergio Menezes and Alicia Kowaltowski
Corresponding author e-mail: alicia@kowaltowski@iq.usp.br

Differently from what one might expect from the textbook representations, mitochondria are not static organelles which are always in well-defined round shapes. In fact, they are highly dynamic organelles which undergo constant cycles of fission and fusion with nearby mitochondria [1]. “mitochondria are not static organelles … in well-defined round shapes” The balance between these fusion and fission events within the cell is what will define the shape of the mitochondrial network, which can range all the way from several separate round shaped mitochondria (high fission, low fusion balance) to very interconnected networks of elongated mitochondria that span throughout the cell (high fusion, low fission balance) [1]. Several factors like cell type, nutrient availability, progression through the cell cycle and even pathological conditions contribute to this fusion/fission balance within the cell [2, 3]. The study of these dynamic modulations of mitochondrial morphology is broadly called "mitochondrial dynamics" [1], and is a field that has received a lot of attention in the last two decades.

In our recent study accepted for publication in The Faseb Journal [preprint available at https://www.biorxiv.org/content/10.1101/624981v1], we show a novel role for mitochondrial dynamics in regulating cellular Ca²⁺ signaling and homeostasis. “we show a novel role for mitochondrial dynamics in regulating cellular Ca²⁺ signaling and homeostasis” Mitochondria forced into a pro-fusion phenotype through the inhibition of the fission protein DRP1 (by competition with a dominant-isoform) presented increased mitochondrial Ca²⁺ uptake rates and maximal uptake capacity, while mitochondria forced to a fission phenotype by the knockdown of the fusion protein MFN2 showed the opposite effect. Mitochondrial Ca²⁺ uptake is a process mediated by the entry of Ca²⁺ ions in the mitochondrial matrix through the protein MCU (mitochondrial calcium uniporter) driven by the negative-inside mitochondrial membrane potential, and has been extensively shown to impact several processes involving Ca²⁺ signaling in the cell [6]. In our work we also show that one of these regulated Ca²⁺ uptake processes, known as store-operated Ca²⁺ entry (a homeostatic mechanism by which cells are capable of replenishing their ER Ca²⁺ stores by promoting extracellular Ca²⁺ entry through the membrane) is modulated by mitochondrial morphology, with more fragmented mitochondria resulting in an impairment of this process, while more fused mitochondria resulted in a faster activation of extracellular Ca²⁺ entry. We also have observed a reduction in basal cytoplasmic and ER Ca²⁺ levels in the cells with more fragmented mitochondria, which was associated with increased levels of ER stress markers, showing that mitochondrial morphology can also regulate these aspects of cellular Ca²⁺ homeostasis.

By showing that the modulation of mitochondrial morphology can impact mitochondrial Ca²⁺ uptake and promote changes in Ca²⁺ homeostasis in the cell, this work establishes a new connection between mitochondrial dynamics and cell signaling.

References

L. Tilokani, S. Nagashima, V. Paupe, J. Prudent. Mitochondrial dynamics: overview of molecular mechanisms Essays In Biochemistry, 62(3): 341–60, 2018. | doi: 10.1042/ebc20170104
M. Liesa, O. Shirihai. Mitochondrial Dynamics in the Regulation of Nutrient Utilization and Energy Expenditure Cell Metabolism, 17(4): 491–506, 2013. | doi: 10.1016/j.cmet.2013.03.002
R. Horbay, R. Bilyy. Mitochondrial dynamics during cell cycling Apoptosis, 21(12): 1327–35, 2016. | doi: 10.1007/s10495-016-1295-5
M. F. Forni, J. Peloggia, K. Trudeau, O. Shirihai, A. J. Kowaltowski. Murine Mesenchymal Stem Cell Commitment to Differentiation Is Regulated by Mitochondrial Dynamics Stem Cells, 34(3): 743–55, 2015. | doi: 10.1002/stem.2248
M. Vig, J. Kinet. Calcium signaling in immune cells Nature Immunology, 10(1): 21–7, 2008. | doi: 10.1038/ni.f.220
A. Spät, G. Szanda, G. Csordas, G. Hajnóczky. High- and low-calcium-dependent mechanisms of mitochondrial calcium signalling Cell Calcium, 44(1): 51–63, 2008. | doi: 10.1016/j.ceca.2007.11.015

Sergio Menezes and Alicia Kowaltowski, from Department of Biochemistry,
Institute of Chemistry, University of São Paulo, Brazil

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Branding in Scientific Publishing

Submitted by redoxoma on Fri, 12/14/2018 - 21:15

The Radical-Free Corner by Alicia Kowaltowski and Ignacio Amigo

A recent Facebook post by a colleague celebrated his publication in the journal Nature Scientific Reports. The publication was important and should be celebrated, except for the small detail that there is, in reality, no journal called Nature Scientific Reports, but instead a journal named Scientific Reports. While this journal is published by Nature Publishing Group - the same company responsible for highly selective titles such as Nature and Nature Medicine - it has a completely different acceptance policy, publishing scientifically valid and technically sound papers, irrespective of impact.

Adding “Nature” to the journal name may seem like an innocent mistake, but we can’t help but notice that many scientists are eager to have their names associated with prestigious periodical brand-names. The practice isn't limited to the Nature brand. For example, Cell Press publishes many Cell-titled journals which carry at least part of the prestige of the trendy high-impact journal Cell, but also produces a handful of journals without “Cell” in their name, including Neuron and Immunity. Scientists are now referring to publications in “Cell journal Neuron”, “Cell Immunity” or similar variations. This constitutes, in our view, an attempt to gain visibility for journals by associating them to prominent scientific brand names.

Scientific journal branding has grown in many ways over the last few years. Publishers of prestigious journals have launched numerous new publication venues using the visibility gained by their flagship journal names. Science Publishing Group, for example, now hosts 13 journals with “Science” as the first name in the title, in addition to the traditional and high-impact Science journal. Eight journals are published under the “Cell” brand name, 14 journals currently contain “The Lancet” in their title (including the highly influential medical journal The Lancet), and an impressive 57 journals have titles that begin with the word “Nature”.

This strategy seems to have worked, as many of these brand name journals are growing very rapidly. For example, Cell Reports was launched in 2012 and published 1040 scientific papers in 2017, an average of 2.8 papers a day. Nature Communications has gone from publishing 156 papers in 2010 to 4288 in 2017, a 2748% increase in seven years, and a current average of 11.7 papers per day. For comparison, Public Library of Science journals such as PLoS Biology and PLoS Medicine, which have similar impact factors and the same open access publishing strategy, publish more modest numbers of 200-300 papers per year.

The growth in publications is not a result of competitive pricing; Cell Reports charges US$ 5000 per paper, while publishing in Nature Communications costs US$ 5700, more than double the median price for open access publishing (US$ 2145, as uncovered by analyzing 894 open access journals with publically available prices). PLoS Biology and PLoS Medicine, on the other hand, charge US$ 3000 per article. PLoS One pioneered the acceptance of scientifically sound articles irrespective of impact, yet it has been surpassed by Scientific Reports as the world’s largest journal, despite the fact that the latter offers the same service at a higher price.

The interest to publish in high-priced brand-name journals could be related to a more careful editorial process. However, our own experience suggests that the editorial process is no better than that of other journals. Indeed, about one third of the evaluations of Nature Communications services posted in Scirev, a journal evaluation website, include complaints about delays in manuscript handling and poor editorial management. We suggest the primary reason for such interest is scientific branding itself. Having a brand name and social media-friendly URL such as Nature, The Lancet, Science or Cell linked to a publication is still a sign of prestige, even if these publishers are widening their audience and becoming increasingly less exclusive.

The shift towards what we call “scientific branding” is happening at the same time as the scientific community is actively discussing means to improve publication standards. Open topics include finding new ways to evaluate quality and impact, as well as using our limited resources – of time and money – in more efficient ways. Associating specific brands and paying high publication costs in exchange for perceived prestige is not a path we should follow.

Alicia Kowaltowski and Ignacio Amigo, from Department of Biochemistry,
Institute of Chemistry, University of São Paulo, Brazil