Methods to study RNA-protein interactions Ramanathan, Muthukumar; Porter, Douglas F; Khavari, Paul A
Nature methods,
03/2019, Letnik:
16, Številka:
3
Journal Article
Recenzirano
Odprti dostop
Noncoding RNA sequences, including long noncoding RNAs, small nucleolar RNAs, and untranslated mRNA regions, accomplish many of their diverse functions through direct interactions with RNA-binding ...proteins (RBPs). Recent efforts have identified hundreds of new RBPs that lack known RNA-binding domains, thus underscoring the complexity and diversity of RNA-protein complexes. Recent progress has expanded the number of methods for studying RNA-protein interactions in two general categories: approaches that characterize proteins bound to an RNA of interest (RNA-centric), and those that examine RNAs bound to a protein of interest (protein-centric). Each method has unique strengths and limitations, which makes it important to select optimal approaches for the biological question being addressed. Here we review methods for the study of RNA-protein interactions, with a focus on their suitability for specific applications.
Optimal management strategies for placenta accreta Eller, AG; Porter, TF; Soisson, P ...
BJOG : an international journal of obstetrics and gynaecology,
April 2009, Letnik:
116, Številka:
5
Journal Article
Recenzirano
Objective To determine which interventions for managing placenta accreta were associated with reduced maternal morbidity.
Design Retrospective cohort study.
Setting Two tertiary care teaching ...hospitals in Utah.
Population All identified cases of placenta accreta from 1996 to 2008.
Methods Cases of placenta accreta were identified using standard ICD‐9 codes for placenta accreta, placenta praevia, and caesarean hysterectomy. Medical records were then ed for maternal medical history, hospital course, and maternal and neonatal outcomes. Maternal and neonatal complications were compared according to antenatal suspicion of accreta, indications for delivery, preoperative preparation, attempts at placental removal before hysterectomy, and hypogastric artery ligation.
Main outcome measures Early morbidity (prolonged maternal intensive care unit admission, large volume of blood transfusion, coagulopathy, ureteral injury, or early re‐operation) and late morbidity (intra‐abdominal infection, hospital re‐admission, or need for delayed re‐operation).
Results Seventy‐six cases of placenta accreta were identified. When accreta was suspected, scheduled caesarean hysterectomy without attempting placental removal was associated with a significantly reduced rate of early morbidity compared with cases in which placental removal was attempted (67 versus 36%, P = 0.038). Women with preoperative bilateral ureteric stents had a lower incidence of early morbidity compared with women without stents (18 versus 55%, P= 0.018). Hypogastric artery ligation did not reduce maternal morbidity.
Conclusions Scheduled caesarean hysterectomy with preoperative ureteric stent placement and avoiding attempted placental removal are associated with reduced maternal morbidity in women with suspected placenta accreta.
Burgeoning availability of genome-wide association study (GWAS) results and national biobank data has led to growing interest in performing multi-trait genetic analyses. Numerous multi-trait GWAS ...methods that exploit either summary statistics or individual-level data have been developed, but their relative performance is unclear. Here we develop a simulation framework to model the complex networks underlying multivariate genetic epidemiology, enabling the vast model space of genetic effects on multiple correlated traits to be explored systematically. We perform a comprehensive comparison of the leading multi-trait GWAS methods, finding: (1) method performance is highly sensitive to the specific combination of genetic effects and phenotypic correlations, (2) most of the current multivariate methods have remarkably similar statistical power, and (3) multivariate methods may offer a substantial increase in the discovery of genetic variants over the standard univariate approach. We believe our findings offer the clearest picture to date of the relative performance of multi-trait GWAS methods and act as a guide for method selection. We provide a web application and open-source software program implementing our simulation framework, for: (i) further benchmarking of multivariate GWAS methods, (ii) power calculations for multivariate genetic studies, and (iii) generating data for testing any multivariate method in genetic epidemiology.
In Australia, we have relied on genomic epidemiology (and associated derived parameters such as viral growth rate, reproductive number, and estimated sampling proportion) to inform public health ...policy changes 1. Genome surveillance alone may not be sufficiently informative to produce meaningful epidemiological estimates. ...we argue here that more genomes do not necessarily mean better results. Sustainable sequencing to track the COVID-19 pandemic Whilst public health and social measures, quarantine restrictions and vaccination have all been utilised in past and current pandemics, the COVID-19 pandemic is the first to employ genomic sequencing on a massive global scale. In both Australia and New Zealand, where the proportion of cases sequenced has been substantial, we have been able to use the data at the “macro” level (studying global evolution of the virus, emergence of VOCs and informing public health policies) and at the “micro” level (inferring local transmission networks and the impact of public health interventions on genomic clusters) 1,6–9.
Abstract
Retinal pigment epithelium (RPE) performs essential functions for ensuring retinal homeostasis and is a key site for pathogenic changes leading to age-related macular degeneration (AMD). ...Compromised proteostasis in RPE results in ER stress and ER stress-dependent antioxidant, apoptosis and autophagic responses. ER stress induces the unfolded protein response (UPR) in which
EIF2AK3,
encoding the protein kinase RNA-like ER kinase (PERK), acts as a key regulator. Downregulated
EIF2AK3
gene expression has recently been identified in AMD using human donor RPE, however the molecular mechanisms that integrate the various ER-mediated cellular pathways underpinning progressive RPE dysfunction in AMD have not been fully characterised. This study investigated the downstream effects of PERK downregulation in response to Brefeldin A (BFA)-induced ER stress in ARPE-19 cells. PERK downregulation resulted in increased ER stress and impaired apoptosis induction, antioxidant responses and autophagic flux. ARPE-19 cells were unable to efficiently induce autophagy following PERK downregulation and PERK presented a role in regulating the rate of autophagy induction. The findings support PERK downregulation as an integrative event facilitating dysregulation of RPE processes critical to cell survival known to contribute to AMD development and highlight PERK as a potential future therapeutic target for AMD.
Colored effluents from textile industries are a problem in many rivers and waterways. Prediction of dye adsorption capacities is important in design considerations. The sorption of three basic dyes, ...namely Basic blue 3, Basic yellow 21, and Basic red 22, onto peat is reported. Equilibrium sorption isotherms have been measured for the three single-component systems. Equilibrium was achieved after 21 days. The experimental isotherm data were analyzed using Langmuir, Freundlich, Redlich–Peterson, Tempkin, and Toth isotherm equations. A detailed error analysis has been undertaken to investigate the effect of using different error criteria for the determination of the single-component isotherm parameters and hence obtain the best isotherm and isotherm parameters which describe the adsorption process. The linear transform model provided the highest
R
2
regression coefficient with the Redlich–Peterson model. The Redlich–Peterson model also yielded the best fit to experimental data for all three dyes using the nonlinear error functions. An extended Langmuir model has been used to predict the isotherm data for the binary systems using the single component data. The correlation between theoretical and experimental data had only limited success due to competitive and interactive effects between the dyes and the dye–surface interactions.
Heterophase homojunction formation in atomically thin 2D layers is of great importance for next-generation nanoelectronics and optoelectronics applications. Technologically challenging, controllable ...transformation between the semiconducting and metallic phases of transition metal chalcogenides is of particular importance. Here, we demonstrate that controlled laser irradiation can be used to directly ablate PdSe2 thin films using high power or trigger the local transformation of PdSe2 into a metallic phase PdSe2–x using lower laser power. Such transformations are possible due to the low decomposition temperature of PdSe2 and a variety of stable phases compared to other 2D transition metal dichalcogenides. Scanning transmission electron microscopy is used to reveal the laser-induced Se-deficient phases of PdSe2 material. The process sensitivity to the laser power allows patterning flexibility for resist-free device fabrication. The laser-patterned devices demonstrate that a laser-induced metallic phase PdSe2–x is stable with increased conductivity by a factor of about 20 compared to PdSe2. These findings contribute to the development of nanoscale devices with homojunctions and scalable methods to achieve structural transformations in 2D materials.
THE STRUCTURE OF THE LOCAL HOT BUBBLE Liu, W.; Chiao, M.; Collier, M. R. ...
The Astrophysical journal,
01/2017, Letnik:
834, Številka:
1
Journal Article
Recenzirano
Odprti dostop
ABSTRACT Diffuse X-rays from the Local Galaxy (DXL) is a sounding rocket mission designed to quantify and characterize the contribution of Solar Wind Charge eXchange (SWCX) to the Diffuse X-ray ...Background and study the properties of the Local Hot Bubble (LHB). Based on the results from the DXL mission, we quantified and removed the contribution of SWCX to the diffuse X-ray background measured by the ROSAT All Sky Survey. The "cleaned" maps were used to investigate the physical properties of the LHB. Assuming thermal ionization equilibrium, we measured a highly uniform temperature distributed around kT = 0.097 keV 0.013 keV (FWHM) 0.006 keV (systematic). We also generated a thermal emission measure map and used it to characterize the three-dimensional (3D) structure of the LHB, which we found to be in good agreement with the structure of the local cavity measured from dust and gas.
PUF (Pumilio/FBF) proteins are RNA-binding proteins and conserved stem cell regulators. The Caenorhabditis elegans PUF proteins FBF-1 and FBF-2 (collectively FBF) regulate mRNAs in germ cells. ...Without FBF, adult germlines lose all stem cells. A major gap in our understanding of PUF proteins, including FBF, is a global view of their binding sites in their native context (i.e., their "binding landscape"). To understand the interactions underlying FBF function, we used iCLIP (individual-nucleotide resolution UV crosslinking and immunoprecipitation) to determine binding landscapes of C. elegans FBF-1 and FBF-2 in the germline tissue of intact animals. Multiple iCLIP peak-calling methods were compared to maximize identification of both established FBF binding sites and positive control target mRNAs in our iCLIP data. We discovered that FBF-1 and FBF-2 bind to RNAs through canonical as well as alternate motifs. We also analyzed crosslinking-induced mutations to map binding sites precisely and to identify key nucleotides that may be critical for FBF-RNA interactions. FBF-1 and FBF-2 can bind sites in the 5'UTR, coding region, or 3'UTR, but have a strong bias for the 3' end of transcripts. FBF-1 and FBF-2 have strongly overlapping target profiles, including mRNAs and noncoding RNAs. From a statistically robust list of 1404 common FBF targets, 847 were previously unknown, 154 were related to cell cycle regulation, three were lincRNAs, and 335 were shared with the human PUF protein PUM2.
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