Histone deacetylases (HDACs) are negative regulators of transcription and have been shown to regulate specific changes in gene expression. In vertebrates, eighteen HDACs have thus far been identified ...and subdivided into four classes (I-IV). Key roles for several HDACs in bone development and biology have been elucidated through in vitro and in vivo models. By comparison, there is a paucity of data on the roles of individual HDACs in osteoclast formation and function. In this study, we investigated the gene expression patterns and the effects of suppressing individual class II (Hdac4, 5, 6, 9, and 10) and class IV (Hdac11) HDACs during osteoclast differentiation. We demonstrated that HDAC class II and IV members are differentially expressed during osteoclast differentiation. Additionally, individual shRNA-mediated suppression of Hdac4, 5, 9, 10 and 11 expression resulted in increased multinucleated osteoclast size and demineralization activity, with little to no change in the overall number of multinucleated osteoclasts formed compared with control shRNA-treated cells. We also detected increased expression of genes highly expressed in osteoclasts, including c-Fos, Nfatc1, Dc-stamp and Cathepsin K. These observations indicate that HDACs cooperatively regulate shared targets in a non-redundant manner.
Bone is a dynamic tissue that must respond to developmental, repair, and remodeling cues in a rapid manner with changes in gene expression. Carefully-coordinated cycles of bone resorption and ...formation are essential for healthy skeletal growth and maintenance. Osteoclasts are large, multinucleated cells that are responsible for breaking down bone by secreting acids to dissolve the bone mineral and proteolytic enzymes that degrade the bone extracellular matrix. Increased osteoclast activity has a severe impact on skeletal health, and therefore, osteoclasts represent an important therapeutic target in skeletal diseases, such as osteoporosis. Progression from multipotent progenitors into specialized, terminally-differentiated cells involves carefully-regulated patterns of gene expression to control lineage specification and emergence of the cellular phenotype. This process requires coordinated action of transcription factors with co-activators and co-repressors to bring about proper activation and inhibition of gene expression. Histone deacetylases (HDACs) are an important group of transcriptional co-repressors best known for reducing gene expression via removal of acetyl modifications from histones at HDAC target genes. This review will cover the progress that has been made recently to understand the role of HDACs and their targets in regulating osteoclast differentiation and activity and, thus, serve as potential therapeutic target.
Estimating the reproducibility of psychological science Aarts, Alexander A.; Nilsonne, Gustav; Zuni, Kellylynn
Science (American Association for the Advancement of Science),
08/2015, Letnik:
349, Številka:
6251
Journal Article
Recenzirano
Odprti dostop
Empirically analyzing empirical evidence
One of the central goals in any scientific endeavor is to understand causality. Experiments that seek to demonstrate a cause/effect relation most often ...manipulate the postulated causal factor. Aarts
et al.
describe the replication of 100 experiments reported in papers published in 2008 in three high-ranking psychology journals. Assessing whether the replication and the original experiment yielded the same result according to several criteria, they find that about one-third to one-half of the original findings were also observed in the replication study.
Science
, this issue
10.1126/science.aac4716
A large-scale assessment suggests that experimental reproducibility in psychology leaves a lot to be desired.
INTRODUCTION
Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. Scientific claims should not gain credence because of the status or authority of their originator but by the replicability of their supporting evidence. Even research of exemplary quality may have irreproducible empirical findings because of random or systematic error.
RATIONALE
There is concern about the rate and predictors of reproducibility, but limited evidence. Potentially problematic practices include selective reporting, selective analysis, and insufficient specification of the conditions necessary or sufficient to obtain the results. Direct replication is the attempt to recreate the conditions believed sufficient for obtaining a previously observed finding and is the means of establishing reproducibility of a finding with new data. We conducted a large-scale, collaborative effort to obtain an initial estimate of the reproducibility of psychological science.
RESULTS
We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available. There is no single standard for evaluating replication success. Here, we evaluated reproducibility using significance and
P
values, effect sizes, subjective assessments of replication teams, and meta-analysis of effect sizes. The mean effect size (r) of the replication effects (
M
r
= 0.197, SD = 0.257) was half the magnitude of the mean effect size of the original effects (
M
r
= 0.403, SD = 0.188), representing a substantial decline. Ninety-seven percent of original studies had significant results (
P
< .05). Thirty-six percent of replications had significant results; 47% of original effect sizes were in the 95% confidence interval of the replication effect size; 39% of effects were subjectively rated to have replicated the original result; and if no bias in original results is assumed, combining original and replication results left 68% with statistically significant effects. Correlational tests suggest that replication success was better predicted by the strength of original evidence than by characteristics of the original and replication teams.
CONCLUSION
No single indicator sufficiently describes replication success, and the five indicators examined here are not the only ways to evaluate reproducibility. Nonetheless, collectively these results offer a clear conclusion: A large portion of replications produced weaker evidence for the original findings despite using materials provided by the original authors, review in advance for methodological fidelity, and high statistical power to detect the original effect sizes. Moreover, correlational evidence is consistent with the conclusion that variation in the strength of initial evidence (such as original
P
value) was more predictive of replication success than variation in the characteristics of the teams conducting the research (such as experience and expertise). The latter factors certainly can influence replication success, but they did not appear to do so here.
Reproducibility is not well understood because the incentives for individual scientists prioritize novelty over replication. Innovation is the engine of discovery and is vital for a productive, effective scientific enterprise. However, innovative ideas become old news fast. Journal reviewers and editors may dismiss a new test of a published idea as unoriginal. The claim that “we already know this” belies the uncertainty of scientific evidence. Innovation points out paths that are possible; replication points out paths that are likely; progress relies on both. Replication can increase certainty when findings are reproduced and promote innovation when they are not. This project provides accumulating evidence for many findings in psychological research and suggests that there is still more work to do to verify whether we know what we think we know.
Original study effect size versus replication effect size (correlation coefficients).
Diagonal line represents replication effect size equal to original effect size. Dotted line represents replication effect size of 0. Points below the dotted line were effects in the opposite direction of the original. Density plots are separated by significant (blue) and nonsignificant (red) effects.
Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available. Replication effects were half the magnitude of original effects, representing a substantial decline. Ninety-seven percent of original studies had statistically significant results. Thirty-six percent of replications had statistically significant results; 47% of original effect sizes were in the 95% confidence interval of the replication effect size; 39% of effects were subjectively rated to have replicated the original result; and if no bias in original results is assumed, combining original and replication results left 68% with statistically significant effects. Correlational tests suggest that replication success was better predicted by the strength of original evidence than by characteristics of the original and replication teams.
•Embryo-larval zebrafish were exposed to two concentrations of oxybenzone.•The low dose oxybenzone caused a two-fold increase in larval metabolic rate.•RNA-sequencing analysis indicated effects on ...metabolism and biological regulation.•Transcriptomics and metabolic rate data was used to parameterize metabolic models.•Simulation of disrupted glycerolipid metabolism explained bioenergetics effects.
Oxybenzone is an emerging aquatic pollutant whose widespread use has contributed to its detection in the surface waters and body-burdens of exposed biota. In this study, the sub-lethal toxicity effects of oxybenzone were studied at the environmentally relevant concentrations of 0.6 and 5.2 µg/L (including 0.01% DMSO as the solvent control). An integrative in vivo and in silico experimental approach was taken to study the effects of exposure on the metabolic physiology of larval zebrafish (Danio rerio) after 7 days of exposure (from 2 to 9 days post fertilization). The use of whole-organism respirometry showed a statistically significant ∼2x increase in metabolic rate for the 0.6 µg/L treatment group, with no significant differences between the solvent control versus 5.2 µg/L oxybenzone treatment level. The analysis of whole-transcriptome RNA-sequencing data showed functional categories related to metabolism (metabolic enzymes) and biological regulation (genome regulation, cell signaling) to be highly dysregulated. The transcriptomics changes for metabolic enzyme genes were used to parameterize in silico stoichiometric metabolic models for each treatment group. Flux balance analysis (FBA) simulations for each metabolic model revealed glycerolipid metabolism to be highly affected under the low dose oxybenzone exposure. The further analysis of core metabolic pathways revealed elevated flux through the esterification reactions of glycerolipid metabolism, producing triglycerides. The elevated in vivo metabolic rate observed for 0.6 µg/L oxybenzone is explainable by the elevated catalytic activities of the esterification reactions. Furthermore, the disruption of glycerolipid metabolism predicted by our in silico analysis agrees with the results of non-targeted metabolomics studies performed by other authors, and which demonstrate oxybenzone exposure to cause dyslipidemia and affect glycerophospholipid metabolism. Therefore, the methods of our study provide a framework for integrated biological pathways-based toxicological analysis.
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