PubMed

FYI:

In contrast to Luciola mingrelica luciferase, in Photinus pyralis luc the homologous mutation Y33H doesn't affect pH-sensitivity of its color (at least there are no any differences in E. coli colonies compared with WT Ppy). Apparently, something is different in the surrounding interactions (it's not particularly surprising given the 67% sequence identity between the P. pyralis and L. mingrelica luciferases).

Regarding this region of the 3D structure, the mutation D234G in Ppy luc comes to mind: it makes Ppy luc quite pH-resistant (hence, greenish colony color with low pH-dependent shift); however, in the fully pH-sensitive L. mingrelica luc the corresponding residue is already G236.

In relation to this article I published a Critical observation, due to the too many similarities to a randomized controlled trial by Wang et al.: https://doi.org/10.1016/j.ijsu.2017.01.019 (http://www.sciencedirect.com/science/article/pii/S1743919117300201)

Our lab has undertaken to map the sites of expression and localization of ENaC and CFTR in epithelial tissues. This article is the second one in the series and it concentrates on the skin.

In the first paper, we covered the sites of localization of ENaC and CFTR in the respiratory tract and the female reproductive tract. Both of these tissues contain large stretches of epithelium covered with multi-ciliated cells. We had shown that in these epithelia with motile cilia, ENaC is expressed along the entire length of the cilia. Reference: https://www.ncbi.nlm.nih.gov/pubmed/22207244

In the current work on the skin, epidermis and epidermal appendages, ENaC was found mostly located in the cytoplasm of keratinocytes, sebaceous glands, and smooth muscle cells. Only in the eccrine type sweat glands, ENaC and CFTR were found predominantly on the luminal membrane facing the lumen of the ducts. Thus, the reuptake of Na+ ions secreted in sweat probably takes place in the eccrine glands.

One sentence was accidentally omitted from the acknowledgments.

We thank all laboratory members for continuing support and constructive discussion and Angelita Alcos for technical support.

Is CoAlation biologically relevant or a non-functional by-product of the chemical reaction between CoA and cysteine thiols in proximal proteins under certain redox conditions?

Firstly, in my opinion the work described here is technically sound. The development of the specific antibody for CoA, and the mass spectrometric method to detect the modification on peptides are key tools in the analysis of any post-translational modification. However, there is a risk when using these super-sensitive methods, that one can detect vanishingly small amounts of modified peptides, which inevitably calls relevance into question. More specifically, modern mass-spectrometry based proteomics in combination with peptide-level enrichment of modified species has allowed us to identify modification sites in the order of tens of thousands for phosphorylation, ubiquitination, acetylation and SUMOylation (as of May 2017). For these fields, the onus of the researcher has very quickly shifted from identification of sites, to evidence for biological meaning. In short, the question is no longer “Which proteins?”, but “Why?”.

Taking acetylation as an example: Phosphositeplus (www.phosphosite.org) lists over 37000 acetylation sites, the majority identified via MS-based proteomics where acetylated peptides have been enriched using acetylated lysine specific antibodies. However, further work investigating endogenous stoichiometry (or site occupancy) of acetylated lysines has revealed that the vast majority are below 1%. Meaning, for most sites, less than 1% of the pool of a protein actually has an acetyl group on a particular lysine (see https://www.ncbi.nlm.nih.gov/pubmed/26358839 and https://www.ncbi.nlm.nih.gov/pubmed/24489116). This clearly calls into question the ability of acetylation to drastically alter the function of most of the proteins identified as ‘targets’.

A very interesting hypothesis is emerging, whereby many of the identified sites of acetylation are not mediated by the specific transfer of acetyl groups via acetyl-transferase enzymes in cells, but are direct acceptors of acetyl groups from reactive chemicals such as acetyl-CoA, or acetyl-phosphate (an earlier review can be found here https://www.ncbi.nlm.nih.gov/pubmed/24725594). This is termed, non-enzymatic, or chemical modification.

Intriguingly, this proximity-based direct modification process may not be restricted to non-enzymatic modification systems. In fact the majority of enzyme-catalysed cellular post-translational modifications involve highly reactive intermediates (such as thioester-bonded ubiquitin or ubiquitin-like modifiers to E1 or E2 enzymes), which can modify lysines in absence of the specificity-determining enzymes (E3 ligases). So it follows that ‘unintended’ modifications can occur for any biologically relevant post-translational modification simply by spatial proximity. This actually also fits with the acetylation site occupancy studies that showed (relatively) higher occupancy in proteins that are themselves involved in acetylation dynamics. Couple these theories with the exquisitely sensitive detection methods used in modern proteomics studies, and we have the potential to create huge lists of modification sites where the proportion with true biological relevance is unknown.

Where does this all fit in with this work describing post-translational modification of cellular proteins with CoA? Reviewing these data bearing the above in mind, it seems the simplest explanation is that non-enzymatic CoAlation occurs in cells when the redox potential has shifted to tip the balance in favour of reaction of CoA with cysteine thiols in proximal proteins. Removal of oxidising agents would allow the balance to revert to more reducing conditions, and so reversal of the CoAlation. The data presented in this paper support this idea as CoAlation is redox-dependent and ‘targets’ proteins that are known to interact with CoA in the cell.

In short, as with many of the published post-translational modification proteomes, much needs to be done to give biological credibility to sites of CoAlation. In particular occupancy calculations and protein-specific evidence that CoAlation regulates function in vivo, will go a long way to putting the notion of biological relevance beyond reasonable doubt. Until then we should consider the possibility that in many cases, post-translational modifications identified by modern methods have the potential to be the unintended consequence of interactions between reactive molecules and nearby proteins. It is worth noting that such a situation does not exclude biological relevance, but it makes finding any very challenging.

Erratum at Fig.7a's legend:

"Low" FDR leads to more specific results but may miss true findings, while "high" FDR is more sensitive but may include false positive findings.

During light chloroform anaesthesia, 1 of 2500 patients succumbed to sudden cardiac syncope – usually when the skin was incised.

1 in 2000 has a genetically determined defect in repolarisation of the myocardium – the long-QT syndrome. Such patients may likewise succumb to sudden cardiac arrest when experiencing emotional and/or physically stressing events.

The striking similarity in the mode of dying – the sudden unexpected arrest of the heart during stress - makes it a fair hypothesis/assumption that patients dying during chloroform anaesthesia were individuals with an inherited or acquired delay in myocardial repolarisation.

No ECG recording from a patient dying during chloroform anaesthesia exists so the hypothesis cannot be proven.

For 100 years, chloroform was used to alleviate labour pain – remarkably with no maternal deaths. A recent investigation has shown an oestradiol-mediated shortening of the QT-interval - both in normal women and in women with the inherited form of delayed myocardial repolarisation - providing a likely explanation for the safety of the obstetric use of chloroform and lends credence to the hypothesis presented in the paper.

P.G.Berthelsen. MD. Charlottenlund, Denmark

Authors names are incorrect, being listed by their given names not their family names. Should be Bao XY, Wong CK, Li EKM, Tam LS, Leung PC, Yin YB, and Lam CWK.

The authors and others might be interested in the following case report from Dr. Nancy Klimas, published in the Journal of Chronic Fatigue Syndrome in 2001. Autologous lymph node transplant was done successfully in one subject with resulting improvements in clinical status and cytokine measurements:

http://www.tandfonline.com/doi/abs/10.1300/J092v08n01_03?journalCode=icfs20

I think that this commentary is well written overall.

Unfortunately, it lacks some important facts that would have assisted the readers' fair judgements.

So, I have posted my post-publication peer review (PPPR), which also contains the aforementioned facts, onto PubPeer (https://pubpeer.com/publications/0BBC818513066058DB929595CE7C32/comments/120820).

It would be strongly recommended to read the PPPR as well before or after reading this commentary, in order to have unbiased opinions on its subjects.

Kiyoshi Ezawa, Ph.D., the author of references [53,54,55], which are a part of the main subjects of the commentary.

Although interesting, this paper is hurt by the narrow possibilities it examines, and by prior work on interstellar communications it overlooks.

Specifically, it does not consider communication methods that require almost no energy from a civilization, but instead use the energy of the civilization's star. For example, page 127 of Stephen Webb's excellent book, "If the Universe is Teeming with Aliens... Where is Everybody?", mentions: (1) Frank Drake's realization that unusual chemical elements, e.g. praseodymium, could be launched into a star to change its spectrum, causing a signal and (2) Philip Morrison's suggestion that matter be placed in orbit around the star so it periodically obscures the star's light output. Both methods would be detectable at long distances, and could be modulated to give clear evidence of life (e.g. modulating in a prime number pattern). Certainly, the success of the Kepler probe proves that Morrison modulation can be detected over interstellar distances.

Thus, Rose and Wright don't ask the right question. Instead of seeking the lowest-energy insterstellar communication method, they should have been seeking the method that demands the lowest energy from a civilization. The best answer to that question seems to be modulation of stellar electromagnetic emissions. Realizing this, our civilization could launch a program called "Stellar Oscillations To Observe Sentience."

The reference URLs were lost along the way, but here they are (have also asked publisher to add these to the online version):

1 - ORI. Guidelines for responsible data management in research. 2006.

2 - DuBois JM, Chibnall JT, Tait R, Vander Wal J. Misconduct: Lessons from researcher rehab.Nature. 2016;534:173–175. doi: 10.1038/534173a. DuBois JM, 2016

3 - ICMJE. Recommendations for the conduct, reporting, editing, and publication of scholarly work in medical journals 2015.

4 - DHHS. Hipaa privacy rule – research. 2013.

5 - NIH. Grants policy statement. Application and Information Processes. 2016.

6 - NIH. NIH data sharing policy. 2007.

In the copy editing process, it appears that several typographical errors were introduced in equations 5, 10, 14, and 15. The corrected equation 5 is:

DeltaBW = [(1-beta) x DeltaEI -Deltadelta x BWinit -(gammaFFM -gammaFM) x FM_init]/(gammaFFM +deltainit +Deltadelta) +[C x (gammaFFM -gammaFM)/(gammaFM +deltainit +Deltadelta)] x LambertW{[(gammaFM +deltainit+Deltadelta) x FMinit]/[C x (gammaFFM +deltainit +Deltadelta)] x Exp[[(gammaFM +deltainit +Deltadelta) x FMinit]/[C x (gammaFFM +deltainit +Deltadelta)]] x Exp[[(1-beta) x DeltaEI - Deltadelta x BWinit]//[C x (gammaFFM +deltainit +Deltadelta)]]}

The corrected Equation 10 is:

DeltaEI = Deltadelta x BWinit/(1-beta) + C² x (gammaFFM-gammaFM) x FMinit/(1-beta) + DeltaBW x (gammaFFM-gammaFM) x C² /(1-beta) x [1+(gammaFM +deltainit +Deltadelta)/(gammaFFM-gammaFM)]-C x (gammaFFM-gammaFM)/(1-beta) x LambertW{C x FMinit x Exp[C x (1 +FMinit) +DeltaBW]}

The corrected Equation 14 is:

DeltaBW=[(1-beta) x DeltaEI -Deltadelta x BWinit]/[gammaFFM +deltainit +Deltadelta-(gammaFFM -gammaFM) x Phi]

The corrected Equation 15 is:

d/dPhi{DeltaBW/DeltaEI} = (gammaFFM -gammaFM) x (1-beta)/[gammaFFM +deltainit-(gammaFFM -gammaFM) x Phi]² > 0

The key points section of this article, the purpose of which is to isolate the ‘key conclusion and implication based on the primary [study] finding(s)’, states that: “A randomized intervention that increased breastfeeding intensity was not associated with reduced obesity”. This is a selective interpretation of the study data on weight status, which show that maternal participation in the PROBIT intervention (which increased breastfeeding exclusivity and duration) was associated with increased odds of offspring having adolescent overweight/obesity (odds ratio=1.14; 1.02-1.28) but not having adolescent obesity (odds ratio=1.09; 0.92-1.29), although it can be seen that both associations were in the same direction. Body mass index (BMI) was also increased in the children from the intervention group by adolescence (mean difference Δ= 0.21, 0.06-0.36).

The reasons for the difference in significance, according to the specified alpha, between the results specifying BMI and unweight/obesity as outcomes vs. those specifying obesity likely arise from the differential power. The relationship of breastfeeding to obesity vs. overweight/obesity had less power, largely due to the lower number of cases (obesity N=589 vs. overweight/obesity N=1868). Simulations in R v3.3.3, suggest the power for has “overweight/obesity” vs. has “obesity” was around 74% vs. 17%. These simulations did not account for the intention to treat procedure nor the correction for data clustering, but due to the effects of these on power being equal across outcomes an assessment of relative power can be made. Even with equal power, the alternative hypothesis was formally tested, but the null hypothesis of “no association” was not, given the absence of any equivalence testing. Positive associations between breastfeeding and offspring adiposity have been reported before, but have not reached statistical significance (see Cope MB, 2008). Therefore, while the association of increased breastfeeding with significantly increased odds of overweight/obesity represents a novel finding which needs to be subjected to replication, without recourse to empirically stronger results, omitting this from the overall interpretation of the study in favor of an untested hypothesis represents a form of bias.

While the manifestation of bias in the article may be small, its effect can still be pernicious. Several organizations, including the World Health Organization and the American Heart Association, state that breastfeeding provides protection against offspring obesity (see WHO report and AHA Fact Sheets). However, this lacks strong statistical justification, given that any inverse associations between breastfeeding and offspring obesity are derived from observational designs and likely to reflect confounding (Kramer MS, 2002), and that probability theory suggests that the breastfeeding-offspring obesity data in the literature as a whole reflect one of two situations: (1) publication bias, or (2) a true positive association between breastfeeding and offspring obesity in at least one other published sample (Cope MB, 2008). That is not to deny that there are a number of valid reasons to support breastfeeding, not related to obesity (Anonymous, 1997). But perhaps it is this which has lead to a problem with ‘white hat bias’ in the breastfeeding-obesity literature - a term coined by Cope and Allison to denote ‘bias leading to the distortion of research based-based information in the service of what may be perceived as righteous ends (Cope MB, 2010). One such reason to support breastfeeding is to enable personal choice for parents and caregivers. However, this is incompatible with the practice of giving misleading information on the benefits of breastfeeding which actually deprives caregivers of their right to make informed decisions about feeding infants.

This is a problematic situation, and needs to be corrected. The causes are unknown, but distorted presentation of data has been identified in multiple reports of randomized clinical trials, often in only one section e.g. the abstract (Boutron I, 2010), and often in the secondary literature, such as press releases (Cope MB, 2010). Therefore all authors need express conclusions with great clarity and consistency, and not selectively include and exclude results without recourse to relative empirical strengths. To be accurate in reporting in this article, the results of this study as a whole are consistent with either (1) an association between breastfeeding and increased offspring overweight/obesity, or (2) a lack of empirical strength in this study to contribute to the debate on whether there is an association between the two constructs.

Should we screen carriers of maternally inherited SDHD mutations?

Jean-Pierre Bayley (1), Jeroen C Jansen (2), Eleonora P M Corssmit (3) and Frederik J Hes (4) 1. Department of Human Genetics, 2. Department of Otorhinolaryngology, 3. Department of Endocrinology and Metabolic Diseases, 4. Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands

We wish to comment on the above paper by Burnichon and colleagues: Burnichon N, et al. Risk assessment of maternally inherited SDHD paraganglioma and phaeochromocytoma. J Med Genet. 2017; 54:125-133. 3

In this paper a prospective study is presented that identified and described development of pheochromocytoma in a carrier of an SDHD mutation. Although at first sight not an uncommon occurrence in carriers of these mutations, this case is unusual because the mutation was inherited via the maternal line. This is now only the third reported case of confirmed phaeochromocytoma development following maternal transmission of an SDHD mutation. (1-3) The patient in question was identified amongst a cohort of 20 maternal mutation carriers who underwent imaging surveillance. Based on the identification of one patient in this cohort (5%), the authors make recommendations for the clinical care of carriers of a maternally inherited SDHD mutation. They advise targeted familial genetic testing from the age of 18 in families with SDHD mutations, and that identified carriers undergo imaging and biochemical workup to detect asymptomatic tumours. If the first workup is negative, the authors suggest that patients be informed about paraganglioma-phaeochromocytoma (PPGL) symptoms and recommend an annual clinical examination and blood pressure measurement, with a new workup indicated in case of symptoms suggestive of PPGL. Although this paper is a meaningful contribution to the literature, we are concerned that the authors base their subsequent clinical recommendations on a relatively small cohort. In a recent study, we described one confirmed case of maternal transmission and concluded that “we consider the increase in risk represented by these reports to be negligible.” (2)

Two reasons underlie this statement. Firstly, the somatic rearrangements underlying the maternal cases identified to date are far more complex (loss of the paternal wild-type SDHD allele by mitotic recombination, followed by loss of the recombined paternal chromosome containing the paternal 11q23 region and the maternal 11p15 region) than the molecular events seen in paternal cases (loss of whole chromosome 11). Secondly, our conclusions were based, implicitly, on many previous studies at our centre over the past three decades in which we described various aspects of the large SDHD cohort collected by us over that period. Genetic aspects of this cohort, and 601 patients with paternally transmitted SDHD mutations, were described by Hensen and co-workers in 2012. (4) As all previous studies suggest that mutations are equally transmissible via the paternal or maternal line, our identification of a single maternal case amongst this cohort suggests that the penetrance of maternally transmitted mutations is very low. Using the calculation employed by Burnichon and colleagues and assuming that at least 600 maternal mutation carriers are alive in the Netherlands, we arrive at an estimate of 0.17% (1/601 = 0.17%), rather than their figure of 5%. In addition to our own cohort, 1000’s of SDHD mutation carriers have been identified world-wide. Assuming that 1 in 20 maternally transmitted mutations result in tumours, many more maternally inherited cases would have come to our attention, even without surveillance.

In our opinion the question of management of maternally inherited SDHD mutations comes down to a risk-benefit analysis. The most obvious implication of the recommendations made by Burnichon and colleagues in our patient population would be the institution of surveillance, with all the attendant practical, financial and psychological burdens for 600 carriers of maternally inherited SDHD mutations in order to identify a single case. Furthermore, SDHD-associated PPGL mortality rates and survival in a Dutch cohort of SDHD variant carriers was not substantially increased compared with the general population. (5) In practice, carriers of maternally inherited SDHD mutations at our centre are not advised to undergo surveillance. Instead, we reassure them that their risk of developing PPGL is exceptionally low (described three times worldwide), but that they should be aware, more so than the general population, of symptoms that are suggestive of paraganglioma or phaeochromocytoma. Many families have been in our care for over 25 years and in that time we have found no evidence to suggest that this policy should be revised.

NB. A version of this comment has been posted on the Journal of Medical Genetics website and has been commented on in turn by Burnichon and colleagues.

References

1.Yeap PM, Tobias ES, Mavraki E, Fletcher A, Bradshaw N, Freel EM, Cooke A, Murday VA, Davidson HR, Perry CG, Lindsay RS. Molecular analysis of pheochromocytoma after maternal transmission of SDHD mutation elucidates mechanism of parent-of-origin effect. J Clin Endocrinol Metab 2011;96:E2009-E2013.

2.Bayley JP, Oldenburg RA, Nuk J, Hoekstra AS, van der Meer CA, Korpershoek E, McGillivray B, Corssmit EP, Dinjens WN, de Krijger RR, Devilee P, Jansen JC, Hes FJ. Paraganglioma and pheochromocytoma upon maternal transmission of SDHD mutations. BMC Med Genet 2014;15:111.

3.Burnichon N, Mazzella JM, Drui D, Amar L, Bertherat J, Coupier I, Delemer B, Guilhem I, Herman P, Kerlan V, Tabarin A, Wion N, Lahlou-Laforet K, Favier J, Gimenez-Roqueplo AP. Risk assessment of maternally inherited SDHD paraganglioma and phaeochromocytoma. J Med Genet 2017;54:125-33.

4.Hensen EF, van DN, Jansen JC, Corssmit EP, Tops CM, Romijn JA, Vriends AH, Van Der Mey AG, Cornelisse CJ, Devilee P, Bayley JP. High prevalence of founder mutations of the succinate dehydrogenase genes in the Netherlands. Clin Genet 2012;81:284-8.

5.van Hulsteijn LT, Heesterman B, Jansen JC, Bayley JP, Hes FJ, Corssmit EP, Dekkers OM. No evidence for increased mortality in SDHD variant carriers compared with the general population. Eur J Hum Genet 2015;23:1713-6.

Implementation errors in the GingerALE Software: Description and recommendations http://onlinelibrary.wiley.com/doi/10.1002/hbm.23342/full

NB to readers: The article itself was not retracted; the journal merely removed its electronic reproduction that had been created in error. See publisher's message below.

This article has been removed: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). Please note that a special edition of Canadian Journal of Diabetes (Volume 39 Supplement 4) was published electronically in error and has since been removed. This edition was planned as a print-only reproduction of a selection of earlier published articles from Canadian Journal of Diabetes: electronic publication of the edition created duplicate items, and were therefore removed. The original articles remain and are unaffected. Andrew Miller, Executive Publisher.

A classic paper by Dr. Salvati that many of my more seasoned colleagues often refer to when discussing palliative treatment of low rectal cancer using serial electrocoagulation.

Unfortunately, the search strategy for this systematic review was not published by the journal. It may be found here.