PubMed

I see the data in Figure 3 confusing and might involve a bias. Figure 1 clearly depicts a stable PS-LTP recorded for 15 minutes every day for successive 14 days. However, in Figure 3b the magnitude of PS-LTP with anisomycin (but without "reactivation" (Sic1)) looks decreasing from the values between 0-3 days, albeit non significantly (I guess the lack of significant differences was due to high SD; the values of SD were not reported in the article but can be seen in the figures). There is no explanation though for that tendency of decreasing PS magnitude compared to stable values depicted in Figure 2. More intriguing is why the recording interval following "reactivation" was restricted to 2 days (total 5 days), which is much shorter than the one depicted in Figure 1 (14 days)?

Figure 1 in this paper is problematic. It states to show survival curves for uveal melanoma patients. However, while there were 13 patients with uveal melanoma of whom 12 were treated, the figure shows 18 deaths.

After asking the FDA for clarification, I was directed to the FDA's Blood Products Advisory Committee Transcript... which states the following "Babesia microti is among the most frequently transfusion transmitted infections reported to FDA, with associated fatalities, for which no donor testing is available."

https://www.fda.gov/downloads/AdvisoryCommittees/CommitteesMeetingMaterials/BloodVaccinesandOtherBiologics/BloodProductsAdvisoryCommittee/UCM449523.pdf

The FDA has labelled the page number 9 (which corresponds to digital page number 11).

So, this statement may have been misinterpreted to mean that "Babesia is the most common transfusion transmitted infection in the United States".

The parameters here are unclear but with the assistance of the laser manufacturer, the following calculation is made: 1. IR Source 905 nm pulsed (pulse duration = 200 ns, adjustable frequency, peak power, according to the frequency of the nominal value (45 W) 2. Continuous visible source 650 nm (output power 70 mW) The peak power (45 W nominal power) depends on the set frequency and it decreases when the frequency increases. The frequency used in the article of 30 kHz (30,000 Hz) is of about 34 Watt. The energetic value reported on the article (48.6 joule) is given from the sum of the contribution of the 2 sources: 1. Source contribution IR 905nm: 34 W200 ns30000 Hz180 sec ≈ 36 joule 2. Source contribution Visible 650nm: 0.07 W180sec = 12.6 joule The weight of a Wistar rat of 5 weeks of age is around 200 g, so a child of 10 years weighting 15 kg, in the need of PBM for the investigated condition would then receive more than 75 times 48.6 J = 3645 J. This, applied seven times during a period of two weeks, would end up in a total applied energy of 25515 J. The relevance of the reported results need to be put into that perspective.

I would like to warn anyone who could be concerned by the appealing title of this paper. There is no serious evidence of an integron integrase activity in this paper. First, there is no description of the used recombination activity assays (authors refer to previous papers) which turns the paper very difficult to follow. For instance, there is no description of the plasmid content. There is a critical absence of control since Table 4 display "excision efficacy" for every assays (no control in absence of integron, absence of integrase, etc). Then, the efficacy of excision (actually, frequency of excision) is determined as being the ratio of negative or positive PCR (this is also unclear) after transformation of several unexplained plasmid in a Streptococcus strain. Therefore the resulting % most probably reflect the efficiency of PCR rather than the % of excision/integration of GC. A very important point not investigated here (no control) is that is remains unsilved whether the recombination of GC is due to the IntI1 activity or IntI-independant recombination. It is noteworthy to mention that authors did not sequence any PCR product to check the specificty of amplifications. Lastly, there are some very significant signs this paper has not been properly reviewed: (i) The paper contains spelling mistakes in the name of bacteria. (ii) The paper has many wrong claims like the Figure 1 (Structure of integron) in which attC are separated from gene cassette of being part of them. Anyone in the integron field knowns that contrariliy to what is written in the Table 1 the G/TTRRRY does not suffice to determine an attC site. Class 1 integron are not associated to Tn7 but Tn21 transposons (L71), a basic in the integron field. (iii) It is very surprising to have not a single quote of any of the numerous papers from D. Mazel team that is the team leading the field of integron recombinations (iv) The paper was received the 7/09, revised (after reviewing?) the 13/09 and accepted the 14/09 which is far to fast to be honest.

I would really appreciate Pubmed to reconsider the indexation of such papers, and maybe of this journal in which such papers are regular (at least in my fields).

This paper is absurd. What possible reason could there be to show that a dose 10,000+ times the normal dose is toxic? Isn't that a given with all known substances? I fear many people would read the abstract or even just the title and conclude that Hibiscus sabdariffa, which is incredibly safe, is dangerous, while in fact this paper supports just how safe it is (when given in reasonable amounts).

The data reviewed here is not really new. The CDC's recommendations for screening and treating pregnant women in 1993 have resulted in a dramatic drop in perinatal chlamydia infection. We have seen only one case of chlamydial ophthalmia at my institution over the past 20 years and no cases of chlamydial pneumonia. We used to see 30-40 cases/year before screening. We have confirmed this by seroepidemiologc studies, one recently published online in Sex Transm Dis (Banniettis N, Thumu S, Weedon J, Szigeti A, Chotikanatis K, Hammerschlag MR, Kohlhoff SA. Seroprevalence of Chlamydia trachomatis in inner-city children and adolescents – implications for vaccine development. Sex Transm Dis, in press, 2017.). This is also confirmed by the observation that chlamydial ophthalmia is still very common in countries, like the Netherlands, that do not screen and treat pregnant women (Rours GIJG, Hammerschlag MR, De Faber JTHN, de Groot R, Verkooyen RP. Chlamydia trachomatis as a cause of neonatal conjunctivitis in Dutch infants. Pediatrics 121:e321-326, 2008.) Canada has discontinued neonatal ocular prophylaxis and will focus on expanded screening. Neonatal ocular prophylaxis in ineffective for prevention of perinatal chlamydial infection as we demonstrated in 1989 (Hammerschlag MR, Cummings CC, Roblin PM, Williams TH, Delke I. Efficacy of neonatal ocular prophylaxis for the prevention of chlamydial and gonococcal conjunctivitis. New Engl J Med 320:769-72, 1989.). At this point there is so little neonatal chlamydial infection in the US that treatment trials are not really possible.

The NEUROKININ 1 RECEPTOR, a.k.a NK1R SUBSTANCE P RECEPTOR and TACR1, has a cytogenetic location on autosome 2 (2p12). The authors report in Table 1 that their 55 "SIDS" cases were 33 male and 22 female, apparently not noticing that the male fraction of 0.60 they do not report, is virtually identical to the SIDS male fraction of almost all SIDS cohorts pooled together. It has been claimed (PMID 5129451) that such consistency must be related to a recessive X-linkage that doesn't exist for this NK1R receptor.

The reason why the reduction in breast cancer mortality is overestimated is because the reason for the lack of efficiency of mammography screening in termes of mortality reduction has not been understood. As cancers are detected by mammography more than one year before physical examination, this must translate in a strong decrease in mortality. The fact that this strong decrease is not observed is due to the fact that mammography leads to a strong increase in cancer incidence (mistakenly considered as overdiagnosis). The barrier I see relates to information about the actual risks of low-dose irradiation.

Not apparent from the record above, this is a substantial shift (in terms of the conclusions) from an earlier version of the same analysis, here: Jakobsen JC, 2017

Conclusions revised, here Jakobsen JC, 2017

Hdac9 gene encode different isoforms. it would be interesting to know which isoform miR-182 is targeting and whether such interaction occurs in humans.

The findings described here are controversial. Others who analyzed the same sequence data did not reach the same conclusions - and some of the latter report's authors are also involved in another recent study suggesting evolutionary stasis in children receiving suppressive antiretroviral therapy Van Zyl GU, 2017. It will be important to address these discrepancies, because they address issues central to treatment efficacy and HIV cure.

Would the authors (or editors) comment on: a) the variance between outcomes registered on ClinicalTrials.gov, those reported in the published manuscript, and those described in the protocol appended as an electronic supplemental file. b) the absence of a formal sample size estimate from the published report (CONSORT 7a) or the protocol (SPIRIT 14). Thank you.

Since GSK-3alpha is equally inhibited by lithium, the power of this study may have been increased if phosphorylation of Serine 21 of the alpha isoform had been measured too.

Editors' competencies and editing terminology: a call for improved dialog between two worlds of editors

Moher et al. offer a detailed list of competencies for “scientific editors,” by which they mean editors of scientific (particularly biomedical) journals. As they explain (with difficulty) in the first sentence, these are editors who set journal policy, oversee the peer review process, and choose manuscripts for publication. In common parlance, these are editors-in-chief, associate editors, and managing editors.

The authors acknowledge that their list of competencies may also be “useful to other types of editors at biomedical journals, such as technical editors (i.e., those responsible for substantial editing of manuscripts, including re-writing for clarity and language)”. Editors who work “at ... journals” are (or were—few remain today) usually called copyeditors or manuscript editors (as opposed to journal editors). Those few who are still employed by prestigious or well-funded journals may choose to call themselves technical editors, but technical editing and technical writing are terms used (especially in the US) to mean the preparation of reports for technical companies.

Moher et al. do not acknowledge another type of increasingly important editor, namely the authors' editor—one who edits manuscripts before they are submitted to journals and, often, between peer review and acceptance. These editors, who do not work at journals, also advise researcher-authors on journal policy, peer review practices and publishing ethics (as does the newly proposed publications officer). Unlike the publications officer, though, authors' editors have a half-century of quiet experience during which they have matured an approach to working with researcher-authors, documented in a large body of (albeit difficult to find) literature. How they edit depends on many factors, but there exists a broadly agreed nomenclature to describe the spectrum of possible activities—called “levels of edit.” These levels range from the superficial proofreading and copyediting, to language editing, substantive editing (not “substantial” editing), and developmental editing (two other pertinent language services are translation and medical writing). Many levels of edit involve the handling of scientific and technical content. Thus authors' editors are scientific editors, too.

Just as it is essential for authors' editors to know about journals' publication policies, it would be useful for journal editors to be familiar with the spectrum of editorial support that researcher-authors use to prepare fit-for-publication manuscripts. This familiarity should begin with an understanding of the editing services offered for sale by journals' very own publishers. It should also include basic knowledge of the levels of edit terminology, an awareness of the settings in which this type of editing is done (e.g. in-house institutional services, freelance professional services, online e-commerce firms), and an appreciation that editing scope and depth (hence, the quality of the edited text) vary greatly depending on the authors' needs and desires, the editors' abilities, the budget and time, and so on. Because authors' editors provide valuable services to researchers worldwide and, consequently, to journal editors, improved dialog between these two worlds of scientific editors will positively impact research publishing.

Disclosure: I have published two books on editorial support for researchers including Editing Research, a book that investigates and documents the work of authors' editors.

The CRISP software is current available at https://github.com/vibansal/crisp instead of the link in the dead link in the abstract.

Is the His6-HA-SUMO1 knock-in mouse a valid model system to study protein SUMOylation?

K.A. Wilkinson^1* , S. Martin² , S.K. Tyagarajan³ , O Arancio⁴ , T.J. Craig⁵ , C. Guo⁶ , P.E. Fraser⁷ , S.A.N. Goldstein⁸ , J.M. Henley^1* .

¹ School of Biochemistry, Centre for Synaptic Plasticity, University of Bristol, Bristol, UK. ² Université Côte d’Azur, INSERM, CNRS, IPMC, France. ³ Institute of Pharmacology and Toxicology, University of Zurich, Switzerland. ⁴ Taub Institute & Dept of Pathology and Cell Biology, Columbia University, New York, NY, USA. ⁵ Centre for Research in Biosciences, University of the West of England, Bristol, UK. ⁶ Department of Biomedical Science, University of Sheffield, Sheffield, UK. ⁷ Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Canada. ⁸ Stritch School of Medicine, Loyola University, Chicago, USA.

*Address for correspondence: kevin.wilkinson@bristol.ac.uk or J.M.Henley@bristol.ac.uk.

Introduction

There is a large and growing literature on protein SUMOylation in neurons and other cell types. While there is a consensus that most protein SUMOylation occurs within the nucleus, SUMOylation of many classes of extranuclear proteins has been identified and, importantly, functionally validated. Notably, in neurons these include neurotransmitter receptors, transporters, sodium and potassium channels, mitochondrial proteins, and numerous key pre- and post-synaptic proteins (for reviews see Henley JM, 2014, Wasik U, 2014, Peng J, 2016, Martin S, 2007, Luo J, 2013, Craig TJ, 2012, Scheschonka A, 2007, Guo C, 2014, Wu H, 2016, Schorova L, 2016). Furthermore, several groups have reported SUMO1-ylated proteins in synaptic fractions using biochemical subcellular fractionation approaches, using a range of different validated anti-SUMO1 antibodies (Martin S, 2007, Feligioni M, 2009, Marcelli S, 2016, Loriol C, 2012) and many studies have independently observed colocalisation of SUMO1 immunoreactivity with synaptic markers (Konopacki FA, 2011, Ghosh H, 2016, Gwizdek C, 2013, Jaafari N, 2013, Hasegawa Y, 2014). Tirard and co-workers (Daniel JA, 2017) directly challenge this wealth of compelling evidence. Primarily using a His6-HA-SUMO1 knock-in (KI) mouse the authors contest any significant involvement of post-translational modification by SUMO1 in the function of synaptic proteins.

On what basis do Daniel et al. argue against synaptic SUMOylation?

Most of the experiments reported by Daniel et al. use a knock-in (KI) mouse that expresses His6-HA-SUMO1 in place of endogenous SUMO1. Using tissue from these mice, followed by immunoprecipitation experiments, they fail to biochemically identify SUMOylation of the previously validated SUMO targets synapsin1a (Tang LT, 2015), gephyrin (Ghosh H, 2016), GluK2 (Martin S, 2007, Konopacki FA, 2011, Chamberlain SE, 2012, Zhu QJ, 2012), syntaxin1a (Craig TJ, 2015), RIM1α (Girach F, 2013), mGluR7 (Wilkinson KA, 2011, Choi JH, 2016), and synaptotagmin1 (Matsuzaki S, 2015). Moreover, by staining and subcellular fractionation, they also fail to detect protein SUMOylation in synaptic fractions or colocalisation of specific anti-SUMO1 signal with synaptic markers. On this basis, they conclude there is essentially no functionally relevant SUMOylation of synaptic proteins.

What are the reasons for these discrepancies?

• Inefficiency of His6-HA-SUMO1 conjugation and compensation by SUMO2/3

A major cause for concern is that there is 20-30% less SUMO1-ylation in His6-HA-SUMO1 KI mice than in wild-type (WT) mice (Daniel JA, 2017, Tirard M, 2012). Moreover, in the paper initially characterising these KI mice, Tirard et al. showed that while total protein SUMO1-ylation is reduced, total SUMO2/3-ylation is correspondingly increased (Tirard M, 2012). Thus, His6-HA-SUMO1 conjugation is significantly impaired and most likely compensated for by increased conjugation by SUMO2/3. Crucially, however, Daniel et al. do not examine modification by SUMO2/3 at any point in their recent study.
Given that SUMO modification is notoriously difficult to detect the 20-30% reduction in His6-HA-SUMO1 compared to wild-type SUMO1 conjugation will make it even more technically challenging. Moreover, this deficit in SUMO1-ylation may well be offset by an increase in SUMO2/3-ylation of individual proteins, but this likely compensation was not tested. Since these deficits alone could explain why Daniel et al. failed to detect SUMO1 modification of the previously characterised synaptic substrate proteins it is surprising that they did not attempt to recapitulate SUMO1-ylation of the target proteins under the endogenous conditions in wild-type systems used in the original papers.

• Lack of functional studies on the substrates they examine

Daniel et al. confine their studies to immunoblotting and immunolabelling. However, these techniques address only one aspect of validating a bone fide SUMO substrate. It is at least as important to examine the effects of target protein SUMOylation in functional assays. Function-based approaches such as electrophysiology or neurotransmitter release assays are not reported or even discussed by Daniel et al. This is an extremely important omission. We argue that simply because SUMO1-ylation of a protein is beneath the detection sensitivity in a model system that exhibits sub-endogenous levels of SUMO1-ylation, does not mean that protein is not a functionally important and physiologically relevant SUMO1 substrate.

• Insensitivity or inadequate use of assay systems

Failure to detect GluK2 SUMOylation

GluK2 is a prototypic synaptic SUMO1 substrate that has been validated in exogenous expression systems, neuronal cultures and rat brain (Martin S, 2007, Konopacki FA, 2011, Chamberlain SE, 2012, Zhu QJ, 2012). Daniel et al. attempt to detect SUMOylation of GluK2 using immunoprecipitation experiments from the His6-HA-SUMO1 KI mice. However, a key flaw in this experiment is that the C-terminal anti-GluK2 monoclonal rabbit antibody used does not recognise SUMOylated GluK2 because its epitope is masked by SUMO conjugation. Thus, due to technical reasons, the experiment shown could not possibly detect SUMOylated GluK2 whether or not it occurs in the KI mice.

Subcellular fractionation and immunolabelling

Daniel et al. perform subcellular fractionation and anti-SUMO1 Western blots to compare His6-HA-SUMO1 KI and SUMO1 knockout (KO) mice. In the KI mice they fail to detect SUMO1-ylated proteins in synaptic fractions. Importantly, however, they do not address what happens in WT mice, which, unlike the KI mice, exhibit normal levels of SUMO1-ylation. While the authors provide beautiful images of SUMO1 immunolabelling in neurons cultured from WT, His6-HA-SUMO1 KI mice and SUMO1 KO mice, in stark contrast to previous reports using rat cultures (Martin S, 2007, Konopacki FA, 2011, Gwizdek C, 2013, Jaafari N, 2013), they detect no specific synaptic SUMO1 immunoreactivity in neurons prepared from WT mice. We note, however, that the nuclear SUMO1 staining in neurons from His6-HA-SUMO1 KI mice is weak, and even weaker in WT neurons. Given that a very large proportion of SUMO1 staining is nuclear, these low detection levels would almost certainly rule out visualisation of the far less abundant, but nonetheless functionally important, extranuclear SUMO1 immunoreactivity.

In conclusion

Given these caveats we suggest that the failure of Daniel et al. to detect synaptic protein SUMO1-ylation in His6-HA-SUMO1 KI mice is due to intrinsic deficiencies in this model system that prevent it from reporting the low, yet physiologically relevant, levels of synaptic protein modification by endogenous SUMO1. In consequence, we question the conclusions reached and the usefulness of this model for investigation of previously identified and novel SUMO1 substrates.

This trial of extending hemodialysis hours and quality of life was discussed on September 12th and September 13th 2017 on #NephJC, the open online nephrology journal club. Introductory comments written by Swapnil Hiremath are available at the NephJC website here .

The highlights of the tweetchat were:

• The study was well-designed and relevant.

• Interpreting the results, can you validly fit a linear model to a questionnaire score?

• Some would argue that including both incident and prevalent patients may have confounded some of the results as LV mass regresses in the first few months after initiation.

• This paper confirmed previous literature that preserving residual renal function is really essential for better outcomes on dialysis and that HD dose should track with this.

• Fluid control may be more important than solute clearance.

Transcripts of the tweetchats, and curated versions as storify will be shortly available from the NephJC website.

Interested individuals can track and join in the conversation by following @NephJC or #NephJC on twitter, liking @NephJC on facebook, signing up for the mailing list, or just visit the webpage at NephJC.com.