Comparison of Storage Conditions for Human Vaginal Microbiome Studies

BACKGROUND: The effect of storage conditions on the microbiome and metabolite composition of human biological samples has not been thoroughly investigated as a potential source of bias. We evaluated the effect of two common storage conditions used in clinical trials on the bacterial and metabolite composition of the vaginal microbiota using pyrosequencing of barcoded 16S rRNA gene sequencing and (1)H-NMR analyses. METHODOLOGY/PRINCIPAL FINDINGS: Eight women were enrolled and four mid-vaginal swabs were collected by a physician from each woman. The samples were either processed immediately, stored at -80°C for 4 weeks or at -20°C for 1 week followed by transfer to -80°C for another 4 weeks prior to analysis. Statistical methods, including Kolmogorovo-Smirnov and Wilcoxon tests, were performed to evaluate the differences in vaginal bacterial community composition and metabolites between samples stored under different conditions. The results showed that there were no significant differences between samples processed immediately after collection or stored for varying durations. (1)H-NMR analysis of the small molecule metabolites in vaginal secretions indicated that high levels of lactic acid were associated with Lactobacillus-dominated communities. Relative abundance of lactic acid did not appear to correlate with relative abundance of individual Lactobacillus sp. in this limited sample, although lower levels of lactic acid were observed when L. gasseri was dominant, indicating differences in metabolic output of seemingly similar communities. CONCLUSIONS/SIGNIFICANCE: These findings benefit large-scale, field-based microbiome and metabolomic studies of the vaginal microbiota

First-Step Mutations for Adaptation at Elevated Temperature Increase Capsid Stability in a Virus

The relationship between mutation, protein stability and protein function plays a central role in molecular evolution. Mutations tend to be destabilizing, including those that would confer novel functions such as host-switching or antibiotic resistance. Elevated temperature may play an important role in preadapting a protein for such novel functions by selecting for stabilizing mutations. In this study, we test the stability change conferred by single mutations that arise in a G4-like bacteriophage adapting to elevated temperature. The vast majority of these mutations map to interfaces between viral coat proteins, suggesting they affect protein-protein interactions. We assess their effects by estimating thermodynamic stability using molecular dynamic simulations and measuring kinetic stability using experimental decay assays. The results indicate that most, though not all, of the observed mutations are stabilizing

Increasing the risk of spontaneous abortion and major malformations in newborns following use of serotonin reuptake inhibitors during pregnancy: A systematic review and updated meta-analysis

<p>Abstract</p> <p>Selective serotonin reuptake inhibitors (SSRIs) are the most frequently used antidepressants during pregnancy. There are conflicting results about their influence on pregnancy outcomes. The goal of this study was to update our previous meta-analysis about pregnancy outcomes following exposure to SSRIs. For this purpose, all relevant databases were searched from 1990 to March 2012 for studies investigating the pregnancy outcomes following exposure to any therapeutic dosage of any SSRI (fluoxetine, paroxetine, citalopram, escitalopram, sertraline, fluvoxamine) during pregnancy. Types of outcome investigated were spontaneous abortion, major malformations, cardiovascular malformations, and minor malformations. A total of 25 studies met our criteria and were included in the meta-analysis. The odds ratio (OD) values are 1.87 (95% CI: 1.5 to 2.33, P< 0.0001) for spontaneous abortion, 1.272 (95% CI: 1.098 to 1.474, P = 0.0014) for major malformations, 1.192 (95% CI: 0.39 to 3.644, P= 0.7578) for cardiovascular malformations, and 1.36 (95% CI: 0.61 to 3.04, P= 0.4498) for minor malformations. The results demonstrated that SSRIs increase the risk of spontaneous abortion and major malformations during pregnancy while they don’t increase the risk of cardiovascular malformations and minor malformations. Our previous meta-analysis only showed an increase in the risk of spontaneous abortion following the use of SSRIs during pregnancy. This might be due to increase in the number of studies included or addition of two new SSRIs (citalopram and escitalopram). The message to researchers is to try considering SSRIs individually during pregnancy to reduce heterogeneity, although all are aware of inevitable limitations to study on pregnant mothers.</p

Many Labs 5: Testing Pre-Data-Collection Peer Review as an Intervention to Increase Replicability

none172siReplication studies in psychological science sometimes fail to reproduce prior findings. If these studies use methods that are unfaithful to the original study or ineffective in eliciting the phenomenon of interest, then a failure to replicate may be a failure of the protocol rather than a challenge to the original finding. Formal pre-data-collection peer review by experts may address shortcomings and increase replicability rates. We selected 10 replication studies from the Reproducibility Project: Psychology (RP:P; Open Science Collaboration, 2015) for which the original authors had expressed concerns about the replication designs before data collection; only one of these studies had yielded a statistically significant effect (p &lt;.05). Commenters suggested that lack of adherence to expert review and low-powered tests were the reasons that most of these RP:P studies failed to replicate the original effects. We revised the replication protocols and received formal peer review prior to conducting new replication studies. We administered the RP:P and revised protocols in multiple laboratories (median number of laboratories per original study = 6.5, range = 3–9; median total sample = 1,279.5, range = 276–3,512) for high-powered tests of each original finding with both protocols. Overall, following the preregistered analysis plan, we found that the revised protocols produced effect sizes similar to those of the RP:P protocols (Δr =.002 or.014, depending on analytic approach). The median effect size for the revised protocols (r =.05) was similar to that of the RP:P protocols (r =.04) and the original RP:P replications (r =.11), and smaller than that of the original studies (r =.37). Analysis of the cumulative evidence across the original studies and the corresponding three replication attempts provided very precise estimates of the 10 tested effects and indicated that their effect sizes (median r =.07, range =.00–.15) were 78% smaller, on average, than the original effect sizes (median r =.37, range =.19–.50).mixedEbersole C.R.; Mathur M.B.; Baranski E.; Bart-Plange D.-J.; Buttrick N.R.; Chartier C.R.; Corker K.S.; Corley M.; Hartshorne J.K.; IJzerman H.; Lazarevic L.B.; Rabagliati H.; Ropovik I.; Aczel B.; Aeschbach L.F.; Andrighetto L.; Arnal J.D.; Arrow H.; Babincak P.; Bakos B.E.; Banik G.; Baskin E.; Belopavlovic R.; Bernstein M.H.; Bialek M.; Bloxsom N.G.; Bodroza B.; Bonfiglio D.B.V.; Boucher L.; Bruhlmann F.; Brumbaugh C.C.; Casini E.; Chen Y.; Chiorri C.; Chopik W.J.; Christ O.; Ciunci A.M.; Claypool H.M.; Coary S.; Colic M.V.; Collins W.M.; Curran P.G.; Day C.R.; Dering B.; Dreber A.; Edlund J.E.; Falcao F.; Fedor A.; Feinberg L.; Ferguson I.R.; Ford M.; Frank M.C.; Fryberger E.; Garinther A.; Gawryluk K.; Ashbaugh K.; Giacomantonio M.; Giessner S.R.; Grahe J.E.; Guadagno R.E.; Halasa E.; Hancock P.J.B.; Hilliard R.A.; Huffmeier J.; Hughes S.; Idzikowska K.; Inzlicht M.; Jern A.; Jimenez-Leal W.; Johannesson M.; Joy-Gaba J.A.; Kauff M.; Kellier D.J.; Kessinger G.; Kidwell M.C.; Kimbrough A.M.; King J.P.J.; Kolb V.S.; Kolodziej S.; Kovacs M.; Krasuska K.; Kraus S.; Krueger L.E.; Kuchno K.; Lage C.A.; Langford E.V.; Levitan C.A.; de Lima T.J.S.; Lin H.; Lins S.; Loy J.E.; Manfredi D.; Markiewicz L.; Menon M.; Mercier B.; Metzger M.; Meyet V.; Millen A.E.; Miller J.K.; Montealegre A.; Moore D.A.; Muda R.; Nave G.; Nichols A.L.; Novak S.A.; Nunnally C.; Orlic A.; Palinkas A.; Panno A.; Parks K.P.; Pedovic I.; Pekala E.; Penner M.R.; Pessers S.; Petrovic B.; Pfeiffer T.; Pienkosz D.; Preti E.; Puric D.; Ramos T.; Ravid J.; Razza T.S.; Rentzsch K.; Richetin J.; Rife S.C.; Rosa A.D.; Rudy K.H.; Salamon J.; Saunders B.; Sawicki P.; Schmidt K.; Schuepfer K.; Schultze T.; Schulz-Hardt S.; Schutz A.; Shabazian A.N.; Shubella R.L.; Siegel A.; Silva R.; Sioma B.; Skorb L.; de Souza L.E.C.; Steegen S.; Stein L.A.R.; Sternglanz R.W.; Stojilovic D.; Storage D.; Sullivan G.B.; Szaszi B.; Szecsi P.; Szoke O.; Szuts A.; Thomae M.; Tidwell N.D.; Tocco C.; Torka A.-K.; Tuerlinckx F.; Vanpaemel W.; Vaughn L.A.; Vianello M.; Viganola D.; Vlachou M.; Walker R.J.; Weissgerber S.C.; Wichman A.L.; Wiggins B.J.; Wolf D.; Wood M.J.; Zealley D.; Zezelj I.; Zrubka M.; Nosek B.A.Ebersole, C. R.; Mathur, M. B.; Baranski, E.; Bart-Plange, D. -J.; Buttrick, N. R.; Chartier, C. R.; Corker, K. S.; Corley, M.; Hartshorne, J. K.; Ijzerman, H.; Lazarevic, L. B.; Rabagliati, H.; Ropovik, I.; Aczel, B.; Aeschbach, L. F.; Andrighetto, L.; Arnal, J. D.; Arrow, H.; Babincak, P.; Bakos, B. E.; Banik, G.; Baskin, E.; Belopavlovic, R.; Bernstein, M. H.; Bialek, M.; Bloxsom, N. G.; Bodroza, B.; Bonfiglio, D. B. V.; Boucher, L.; Bruhlmann, F.; Brumbaugh, C. C.; Casini, E.; Chen, Y.; Chiorri, C.; Chopik, W. J.; Christ, O.; Ciunci, A. M.; Claypool, H. M.; Coary, S.; Colic, M. V.; Collins, W. M.; Curran, P. G.; Day, C. R.; Dering, B.; Dreber, A.; Edlund, J. E.; Falcao, F.; Fedor, A.; Feinberg, L.; Ferguson, I. R.; Ford, M.; Frank, M. C.; Fryberger, E.; Garinther, A.; Gawryluk, K.; Ashbaugh, K.; Giacomantonio, M.; Giessner, S. R.; Grahe, J. E.; Guadagno, R. E.; Halasa, E.; Hancock, P. J. B.; Hilliard, R. A.; Huffmeier, J.; Hughes, S.; Idzikowska, K.; Inzlicht, M.; Jern, A.; Jimenez-Leal, W.; Johannesson, M.; Joy-Gaba, J. A.; Kauff, M.; Kellier, D. J.; Kessinger, G.; Kidwell, M. C.; Kimbrough, A. M.; King, J. P. J.; Kolb, V. S.; Kolodziej, S.; Kovacs, M.; Krasuska, K.; Kraus, S.; Krueger, L. E.; Kuchno, K.; Lage, C. A.; Langford, E. V.; Levitan, C. A.; de Lima, T. J. S.; Lin, H.; Lins, S.; Loy, J. E.; Manfredi, D.; Markiewicz, L.; Menon, M.; Mercier, B.; Metzger, M.; Meyet, V.; Millen, A. E.; Miller, J. K.; Montealegre, A.; Moore, D. A.; Muda, R.; Nave, G.; Nichols, A. L.; Novak, S. A.; Nunnally, C.; Orlic, A.; Palinkas, A.; Panno, A.; Parks, K. P.; Pedovic, I.; Pekala, E.; Penner, M. R.; Pessers, S.; Petrovic, B.; Pfeiffer, T.; Pienkosz, D.; Preti, E.; Puric, D.; Ramos, T.; Ravid, J.; Razza, T. S.; Rentzsch, K.; Richetin, J.; Rife, S. C.; Rosa, A. D.; Rudy, K. H.; Salamon, J.; Saunders, B.; Sawicki, P.; Schmidt, K.; Schuepfer, K.; Schultze, T.; Schulz-Hardt, S.; Schutz, A.; Shabazian, A. N.; Shubella, R. L.; Siegel, A.; Silva, R.; Sioma, B.; Skorb, L.; de Souza, L. E. C.; Steegen, S.; Stein, L. A. R.; Sternglanz, R. W.; Stojilovic, D.; Storage, D.; Sullivan, G. B.; Szaszi, B.; Szecsi, P.; Szoke, O.; Szuts, A.; Thomae, M.; Tidwell, N. D.; Tocco, C.; Torka, A. -K.; Tuerlinckx, F.; Vanpaemel, W.; Vaughn, L. A.; Vianello, M.; Viganola, D.; Vlachou, M.; Walker, R. J.; Weissgerber, S. C.; Wichman, A. L.; Wiggins, B. J.; Wolf, D.; Wood, M. J.; Zealley, D.; Zezelj, I.; Zrubka, M.; Nosek, B. A