PubMed

The unfolded protein response (UPR) is a conserved pathway that senses stress in the endoplasmic reticulum (ER) and responds to it by eliciting a transcriptional response. Mechanistically, when the stress sensor IRE1 is activated by the accumulation of unfolded proteins in the ER, its cytosolic RNAse domain cleaves the messenger of a transcription factor (Xbp1 in mammals, Hac1 in yeast) at two precise positions, removing an inhibitory intron. The 5' and the 3' parts of the messenger are then re-ligated together, to encode a functional transcription factor that takes part in the response. While the ligase involved in the last processing step was known in yeast, it evaded identification for years in mammals.

Here, the mammalian ligase is identified using a clever trick. A synthetic construct consisting of a Cre recombinase fused to Xbp1 is not expressed in normal conditions, but upon ER stress, Xbp1 is spliced and Cre recombinase is produced. The induction of the recombinase can be easily monitored using a Cre-induced proapoptotic factor, which kills the cells. Using this synthetic circuit, the authors screen a lentiviral RNA interference (RNAi) library and identify hits that fail to induce Cre upon acute ER stress, by simply scoring for survival. They identify the ligase RtcB, which, as with the yeast UPR ligase Trl1, is also involved in tRNA splicing.

This paper presents some spectacular features of membrane chemistry. If you are not into the topic, watching some of the featured movies will likely pique your interest.

It has long been known that different lipid species can have different affinity for each other, such that they may segregate into different phases, which can be visualized as subdomains on artificial membranes such as giant unilamellar vesicles (GUVs). Because a phase-separated membrane has a much lower entropy than a mixed one, phase separation can be achieved by lowering the temperature or increasing order in the membrane by stretching it.

In this paper, the authors bathed GUVs in a hypotonic solution. Because these GUVs are semi-permeable to water, they swell until they eventually rupture, causing a catastrophic leak that re-equilibrates pression. After the GUVs recover from rupture, they start swelling again, and go through several cycles of swelling-rupture until reaching osmotic equilibrium.

Here, the authors observe that, while in relaxed GUVs lipids are perfectly mixed, swelled GUVs show lipid phase separation. Mixing occurs right after each membrane rupture event; therefore, a cycle of separation-mixing follows the cycle of swelling-rupture of the GUV.

It was previously known that vesicles underwent cycles of swelling-rupture. It was also previously known that membrane tension favored lipid phase separation. It is also not clear whether these phenomena are relevant in the case of biological systems. Nonetheless, the movies presented here are spectacular and unveil unexpected and very complex dynamic behaviors of seemingly very simple chemical systems.

English translation of this paper is available at: http://www.mv.helsinki.fi/home/hemila/T2.pdf

English translation of this paper is available at: http://www.mv.helsinki.fi/home/hemila/T4.pdf

English translation of this paper is available at: http://www.mv.helsinki.fi/home/hemila/T6.pdf

In Figure 5A of this paper, the upper part of the panel showing the SKBR3 cells with the FoxM1 plasmid (FC) looks very similar to the panel of MCF-7 cells in Figure 5C of the paper in the Journal of Cellular Biochemistry 108:916-925 published in 2009.

In Fig. 6C, the bottom of the panel showing control (NS) SUM149 cells on the left, looks very similar to the upper part of the panel of UC/FS SUM149 cells on the right.

As some of these panels therefore do not appear to be correctly labelled, the conclusions might not be correct.

For all the reasons given by Hilda Bastian (and a few more, like P = 0.04 provides lousy evidence) it astonishes me that this study should have been trumpeted as though it represented a great advance. That's the responsibility of Nature Neuroscience (and, ultimately, of the authors).

I wonder whether what happens is as follows. Authors do big fMRI study. Glamour journal refuses to publish without functional information. Authors tag on a small human study. Paper gets published. Hyped up press releases issued that refer mostly to the add on. Journal and authors are happy. But science is not advanced.

I certainly got this impression in another recent fMRI paper in Science. Brain stimulation was claimed to improve memory (P = 0.043)

I guess these examples are quite encouraging for those who think that expensive glamour journals have had their day. Open access and open comments are the way forward.

From the title of this editorial I expected a critique of proponents of controversial gain-of-function (GOF) experiments. Perversely, it levels criticism only at the other side of the debate. According to the editorial, opponents of these experiments have used the possibility of a global pandemic (caused by laboratory-produced virus) as a rhetorical device that is so frightening that it trumps reason. It ignores the fact that proponents of these experiments have always invoked the dangers of a deadly (natural) global pandemic to argue that the experiments are critical for human health.

"In the GOF debate," the editorial states, "the repeated mention of the likelihood of a pandemic is an apocalyptic rhetorical device." Perhaps it is, but who in the debate uses this device? The proponents of GOF experiments clearly do. The specter of a devastating pandemic is central, for example, to Yoshihiro Kawaoka's defense of his experiments. He tells us of the frighteningly high rate of death among confirmed H5N1 infections, and writes that

"Within the past century, 'Spanish' influenza, which stemmed from a virus of avian origin, killed between 20 million and 50 million people. Because H5N1 mutations that confer transmissibility in mammals may emerge in nature, I believe that it would be irresponsible not to study the underlying mechanisms."

Similarly, an Erasmus Medical Center press release about work by Ron Fouchier and colleagues bears the headline "Avian influenza could evolve into dangerous human virus", tells us that "The discovery is important as it could prevent a severe pandemic from occurring", and suggests a 60% death rate for H5N1 infection. A piece by Fouchier and others cites the same death rate data and suggests that the toll of an H5N1 pandemic would exceed that of the H1N1 pandemic of 1918. Many additional examples could be mentioned. This side of the debate repeatedly invokes the danger of a deadly pandemic, and presents GOF experiments as necessary for our rescue from this danger.

(It should be noted that the high death rate for H5N1 infection has been called into question. Some defenders of GOF experiments have used diminished estimates of lethality to downplay the danger of the laboratory-produced viruses, usually failing to note that they would also weaken the original argument for the importance of the experiments.)

It was quite reasonable for critics to ask whether GOF experiments are more likely to cause a global pandemic than prevent one. The critics' discussions of pandemics have generally been no more apocalyptic than those of the proponents, such as those referred to above. The editorial's accusations concerning misleading rhetoric are at best one-sided, and arguably are pointed in exactly the wrong direction.

A version of this paper is available, freely and openly, in arXiv: http://arxiv.org/abs/1401.5130

In evaluating the results of this trial it is important to note that the published results do not correspond to the primary outcomes specified in the trial’s original and updated registrations on ClinicalTrials.gov. The four primary outcome measures initially registered (10/7/2008) were: MADRS at 40 minutes, 120 minutes, 24 hours, and 7 days. These were expanded on 1/12/11 to include the MADRS at 240 minutes, 48 hours, 72 hours, biweekly for up to 4 weeks, and early termination. After publication (1/30/14) all Primary Outcomes except MADRS at 24 hours were removed from the ClincalTrials.gov registration. These changes can be tracked at: http://clinicaltrials.gov/archive/NCT00768430 It would be important to understand why the authors changed the outcome measures several times during the trial. These changes are not mentioned in the publication. The finding that ketamine, a dissociative anesthetic that is abused for its euphoric and other mind-altering properties, transiently suppresses MADRS scores is not surprising. It would be much more important clinically to demonstrate significant effects on the outcome measures at 2 to 4 weeks. These were not presented.

The potato hinge protein has a perfect CX9CX3C----CX3CX9C motif which by homology with vertebrate structures should form a helix hairpin with disulfides holding the two arms together. This is the motif recognized by the MIA40/CHCHD4 disulfide relay import system. And like other MIA40 substrates, the hinge protein ends up in the inter-membrane space (attached to cyt c1 of the bc1 complex). I wonder if anyone has checked whether Hinge is imported by the MIA40 system.

In vertebrates one of the middle cysteines is lost, some residues are inserted, spoiling the perfect cannonical MIA40 import sequence. Only two disulfides are formed, and there is a short leader sequence although it is not a typical mitochondrial targeting sequence.

In Saccharomyces, all but two of the cysteines are lost, and the hairpin is clamped by a single disulfide. Could this represent a switch from one import mechanism to another over the course of evolution?

The authors write, "Only two cases of an abdominal pregnancy combined with an intrauterine pregnancy has been reported [11, 12]."

Zacchè MM, 2011 is an additional recent case that the authors did not cite. In addition Reece EA, 1983 is a review of 589 cases of combined intrauterine and extrauterine gestations. A Chinese article Wu X, 1999 also tackles similar cases.

To All,

When I was comparing the relative position of the 64 codons of the Genetic Code between two x-y 2-D Tables, i.e., while keeping the axis Y constant with the C-Rings of the DNA Nucleotides and changing the axis X from having their H-bonds in one Table to their Tautomerism in the other Table, what resulted of this comparison, as my article demonstrates, were the directional arrows of the ancient Chinese representation of the Yin and the Yang (external long arrows at opposite directions annealed to the two internal broken arrows per each of the long ones). When I added the third Table with the third possible comparison of these DNA-Nucleotide properties (i.e., H-bonds in axis X and Tautomerism in axis Y), what I had was the half of a Cube, and by adding the remaining three reciprocal Tables, I was able to complete a Cube. From here, it was not difficult to Spherize such Cube in order to obtain the Spherical representation of the genetic code!

This is my graphic representation of one of the Spherized sides of the Cube: Spherical Genetic Code

Attentively,

Fernando Castro-Chavez. 10/24/2014 Houston, TX

Genomic DNA sequences for the Canton-S and w1 strains studied in this paper have not been deposited in the Short Read Archive. The GEO accession given in the paper (GSE25180 corresponding to SRA accession SRP004442) only contains RNA-seq data, but not DNA-seq data. DNA-seq data for these strains can be obtained from the authors' website at: http://www.eisenlab.org/dosage/data/Reads/Genomic/

One of my students did a similar study for her dissertation (currently in press). She found that the consumption of alchohol is the single biggest cause for car crashes in Turkey (35% of all crashes were associated with alcohol use). This finding is no suprise by itself and complements numerous previous studies. However, she did find a very interesting new correlation. Since her group uses anonymized data from insurance companies, they were able to test several hypothesis which were in coordance with car crashes caused by the consumption of alcohol. For example, she found that certain car brands are associated with a 75% increase in alcohol related car crashes. While this is most likely just correlational and not caused because these cars are harder to drive when under influence, she did find another correlation which might be very intruiging to study further.

Because most of her data was provided by insurance companies, they were very detailed and trustable. For example, they included police reports were applicable. Because of this data they were able to establish wether the alcoholic user was the perpetrator of these crashes or wether (while driving under influence is technically illegal) were the culprit of these crashes. In the vast majority of cases the drivers under the influence of alcohol were indeed the perpetrator (85%). However she did a very intruiging finding when digging deeper in the data that was provided by insurance companies. The use of dashcams Wikipedia has gained a lot of popularity in Turkey in recent years. This is caused by multiple factors, one of which has to do with reduced insurance costs by car insurance companies. When my student corrected for the use of a dashcam, she found dat the pepetrator/culprit(85%/15%) ratio decreased significantly to 55/45%. Of course this is a very intruiging finding which can be caused be several factors. This is the first research to examine the use of a dashcam in relation to the amount of alcohol related car crashes. We're currently looking to see wether these results hold up in a bigger sample size. While this is the first study to find this correlation, there is a previous Dutch one (Website) which found that the use of a dashcam is associated with a reduction of the involvement in general car crashes of 34%. Incidentally, our study showed the same result in alcohol related crashes, but further study is now urgently needed.

LATS protein kinases function in the Hippo signalling system. They are basophilic kinases known to phosphorylate sites that match Hx[Rk]xx[ST] motifs. The requirement for a His residue marks out LATS from other AGC group basophilic kinases. LATS substrate proteins usually have multiple matches to these motifs, as for example YAP1 (human) and SSD1 (yeast). In these proteins the LATS P-sites are in regions of natively disordered polypeptide.

The LATS substrate reported here, Snail1 does have two matches to the LATS site as shown in Fig. 3

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3252572/figure/f3/

But these lie within DNA-binding zinc finger domains. The His residues are part of the zinc coordinating residues that hold the domain in a folded conformation. So long as the zinc fingers are folded, these His sidechains are unavailable to access a kinase active site cleft. Indeed all the residues in the proposed site(s) are in alpha helices when the zinc fingers are folded. The H, R and T residues are conserved in many other zinc finger proteins. If Snail1 zinc fingers can be phosphorylated by LATS then many other zinc finger proteins should also be targets. Because of the restricted focus of the HIPPO signalling pathway and the limited number of known LATS substrates in fly, yeast and mammal systems, this might be unlikely.

In the absence of biophysical data showing that the Snail1 sites can become accessible under plausible phosphorylation conditions, they are considered to be false positive sites in our ELM resource entry for LATS kinases

http://elm.eu.org/elms/elmPages/MOD_LATS_1.html