The impact of functional combined anteversion on hip range of motion: a new optimal zone to reduce risk of impingement in total hip arthroplasty.

Aims: Pelvic tilt (PT) can significantly change the functional orientation of the acetabular component and may differ markedly between patients undergoing total hip arthroplasty (THA). Patients with stiff spines who have little change in PT are considered at high risk for instability following THA. Femoral component position also contributes to the limits of impingement-free range of motion (ROM), but has been less studied.

Highly Satisfied Total Knee Arthroplasty Patients Display a Wide Range of Soft Tissue Balance.

Soft tissue balancing while crucial for a successful total knee arthroplasty (TKA) is incompletely defined and the subject of broad recommendations. We analyzed 69 unilateral computer-assisted surgery posterior stabilized (PS) TKA subjects who postoperatively scored ≥36 out of a possible 40 points on the satisfaction section of the American Knee Society score (2011). We examined a range of postoperative coronal plane laxity parameters and the correlation between preoperative and postoperative laxity.

Insights into the mechanisms of eukaryotic translation gained with ribosome profiling.

The development of Ribosome Profiling (RiboSeq) has revolutionized functional genomics. RiboSeq is based on capturing and sequencing of the mRNA fragments enclosed within the translating ribosome and it thereby provides a 'snapshot' of ribosome positions at the transcriptome wide level. Although the method is predominantly used for analysis of differential gene expression and discovery of novel translated ORFs, the RiboSeq data can also be a rich source of information about molecular mechanisms of polypeptide synthesis and translational control.

Comparative survey of the relative impact of mRNA features on local ribosome profiling read density.

Ribosome profiling (Ribo-seq), a promising technology for exploring ribosome decoding rates, is characterized by the presence of infrequent high peaks in ribosome footprint density and by long alignment gaps. Here, to reduce the impact of data heterogeneity we introduce a simple normalization method, Ribo-seq Unit Step Transformation (RUST). RUST is robust and outperforms other normalization techniques in the presence of heterogeneous noise.

RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data.

Ribosome profiling (ribo-seq) is a technique that uses high-throughput sequencing to reveal the exact locations and densities of translating ribosomes at the entire transcriptome level. The technique has become very popular since its inception in 2009. Yet experimentalists who generate ribo-seq data often have to rely on bioinformaticians to process and analyze their data.

The effect of heterogeneous Transcription Start Sites (TSS) on the translatome: implications for the mammalian cellular phenotype.

Background: The genetic program, as manifested as the cellular phenotype, is in large part dictated by the cell's protein composition. Since characterisation of the proteome remains technically laborious it is attractive to define the genetic expression profile using the transcriptome. However, the transcriptional landscape is complex and it is unclear as to what extent it reflects the ribosome associated mRNA population (the translatome).

Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes.

Background: Oxygen and glucose metabolism play pivotal roles in many (patho)physiological conditions. In particular, oxygen and glucose deprivation (OGD) during ischemia and stroke results in extensive tissue injury and cell death.

Results: Using time-resolved ribosome profiling, we assess gene expression levels in a neural cell line, PC12, during the first hour of OGD.

Translation of 5' leaders is pervasive in genes resistant to eIF2 repression.

Eukaryotic cells rapidly reduce protein synthesis in response to various stress conditions. This can be achieved by the phosphorylation-mediated inactivation of a key translation initiation factor, eukaryotic initiation factor 2 (eIF2). However, the persistent translation of certain mRNAs is required for deployment of an adequate stress response.

GWIPS-viz: development of a ribo-seq genome browser.

We describe the development of GWIPS-viz (http://gwips.ucc.ie), an online genome browser for viewing ribosome profiling data.

rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments.

Motivation: Ribosome profiling is a new technique that allows monitoring locations of translating ribosomes on mRNA at a whole transcriptome level. A recent ribosome profiling study demonstrated that internal Shine-Dalgarno (SD) sequences have a major global effect on translation rates in bacteria: ribosomes pause at SD sites in mRNA. Therefore, it is important to understand how SD sites effect mRNA movement through the ribosome and generation of ribosome footprints.