PhysBinder: Improving the prediction of transcription factor binding sites by flexible inclusion of biophysical properties.

The most important mechanism in the regulation of transcription is the binding of a transcription factor (TF) to a DNA sequence called the TF binding site (TFBS). Most binding sites are short and degenerate, which makes predictions based on their primary sequence alone somewhat unreliable. We present a new web tool that implements a flexible and extensible algorithm for predicting TFBS. The algorithm makes use of both direct (the sequence) and several indirect readout features of protein-DNA complexes (biophysical properties such as bendability or the solvent-excluded surface of the DNA). This algorithm significantly outperforms state-of-the-art approaches for in silico identification of TFBS. Users can submit FASTA sequences for analysis in the PhysBinder integrative algorithm and choose from >60 different TF-binding models. The results of this analysis can be used to plan and steer wet-lab experiments. The PhysBinder web tool is freely available at http://bioit.dmbr.ugent.be/physbinder/index.php.

A novel clinical test for assessing patellar cartilage changes and its correlation with magnetic resonance imaging and arthroscopy.

Controversy still exists regarding the best clinical assessment test for chondromalacia patellae (CMP). Our study aims to evaluate the specificity and sensitivity of a novel clinical test for CMP, the "Patella Slide Test" (PST) against the findings of magnetic resonance imaging (MRI) and arthroscopy. We included 221 consecutive patients planned for elective knee arthroscopic surgery. An MRI scan of the symptomatic knee was performed prior to surgery. On the day of surgery, each patient was examined using the PST followed by a knee arthroscopy to assess the quality of the chondral surfaces of the patellofemoral joint. The MRI and PST results were compared against the arthroscopic findings that served as the gold standard. The PST (0.89) was statistically more sensitive than MRI (0.67) in diagnosing CMP. The PST (0.89) also had a greater negative predictive value (NPV) than MRI (0.74). However, MRI (0.94) was more specific than the PST (0.85). The differences in accuracy and positive predictive value of the PST versus MRI were not statically significant. In conclusion, the PST shows high sensitivity and has a greater NPV than MRI as a clinical test for diagnosing CMP.

Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human.

Gene fusion occurs when two or more individual genes with independent open reading frames becoming juxtaposed under the same open reading frame creating a new fused gene. A small number of gene fusions described in detail have been associated with novel functions, for example, the hominid-specific PIPSL gene, TNFSF12, and the TWE-PRIL gene family. We use Sequence Similarity Networks and species level comparisons of great ape genomes to identify 45 new genes that have emerged by transcriptional readthrough, that is, transcription-derived gene fusion. For 35 of these putative gene fusions, we have been able to assess available RNAseq data to determine whether there are reads that map to each breakpoint. A total of 29 of the putative gene fusions had annotated transcripts (9/29 of which are human-specific). We carried out RT-qPCR in a range of human tissues (placenta, lung, liver, brain, and testes) and found that 23 of the putative gene fusion events were expressed in at least one tissue. Examining the available ribosome foot-printing data, we find evidence for translation of three of the fused genes in human. Finally, we find enrichment for transcription-derived gene fusions in regions of known segmental duplication in human. Together, our results implicate chromosomal structural variation brought about by segmental duplication with the emergence of novel transcripts and translated protein products.

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference.

Placental mammals comprise three principal clades: Afrotheria (e.g., elephants and tenrecs), Xenarthra (e.g., armadillos and sloths), and Boreoeutheria (all other placental mammals), the relationships among which are the subject of controversy and a touchstone for debate on the limits of phylogenetic inference. Previous analyses have found support for all three hypotheses, leading some to conclude that this phylogenetic problem might be impossible to resolve due to the compounded effects of incomplete lineage sorting (ILS) and a rapid radiation. Here we show, using a genome scale nucleotide data set, microRNAs, and the reanalysis of the three largest previously published amino acid data sets, that the root of Placentalia lies between Atlantogenata and Boreoeutheria. Although we found evidence for ILS in early placental evolution, we are able to reject previous conclusions that the placental root is a hard polytomy that cannot be resolved. Reanalyses of previous data sets recover Atlantogenata + Boreoeutheria and show that contradictory results are a consequence of poorly fitting evolutionary models; instead, when the evolutionary process is better-modeled, all data sets converge on Atlantogenata. Our Bayesian molecular clock analysis estimates that marsupials diverged from placentals 157-170 Ma, crown Placentalia diverged 86-100 Ma, and crown Atlantogenata diverged 84-97 Ma. Our results are compatible with placental diversification being driven by dispersal rather than vicariance mechanisms, postdating early phases in the protracted opening of the Atlantic Ocean.

Effect of prehabilitation on the outcome of anterior cruciate ligament reconstruction.

BACKGROUND: Prehabilitation is defined as preparing an individual to withstand a stressful event through enhancement of functional capacity. HYPOTHESIS: We hypothesized that a preoperative exercise program would enhance postoperative outcomes after anterior cruciate ligament reconstruction (ACLR). STUDY DESIGN: Randomized controlled clinical trial; Level of evidence, 1. METHODS: Twenty volunteers awaiting ACLR were randomly assigned to a control or exercise intervention group. The exercise group completed a 6-week gym- and home-based exercise program. Assessments include single-legged hop test; quadriceps and hamstring peak torque and magnetic resonance imaging cross-sectional area (CSA); Modified Cincinnati Knee Rating System score; and muscle biopsy of the vastus lateralis muscle completed at baseline, preoperatively, and 12 weeks postoperatively. Myosin heavy chain (MHC) isoforms protein and messenger RNA (mRNA) expression were determined with SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) and RT-PCR (real-time polymerase chain reaction), respectively; IGF-1 (insulin-like growth factor 1), MuRF-1 (muscle RING-finger protein-1), and MAFbx (muscle atrophy f-box) mRNA expression were determined with quantitative RT-PCR. RESULTS: Following 6 weeks of exercise intervention, the single-legged hop test results improved significantly in the exercise-injured limb compared with baseline (P = .001). Quadriceps peak torque in the injured limb improved with similar gains in CSA compared with baseline (P = .001). However, this was not significantly increased compared with the control group. Quadriceps and vastus medialis CSA were also larger in the exercise group than in controls (P = .0024 and P = .015, respectively). The modified Cincinnati score was better in the exercise-injured limb compared with baseline. At 12 weeks postoperatively, the rate of decline in the single-legged hop test was reduced in the exercise group compared with controls (P = .001). Similar trends were not seen for quadriceps peak torque and CSA. The vastus medialis CSA had regressed to similar levels as the control group (P = .008). The modified Cincinnati score continued to increase in the exercise group compared with controls (P = .004). The expression of the hypertrophic IGF-1 gene was significantly increased after the exercise intervention (P = .028), with a decrease back to baseline 12 weeks postoperatively (P = .012). Atrophic MuRF-1 gene expression was decreased after intervention compared with baseline (P = .05) but increased again at 12 weeks postoperatively (P = .03). The MAFbx levels did not change significantly in either group and within each time point. On the mRNA level, there was a shift from MHC-IIx isoform to MHC-IIa after exercise, with significant changes compared with control preoperatively (P = .028). Protein testing was able to reproduce this increase for MHC-IIa isoform expression only. CONCLUSION: The 6-week progressive prehabilitation program for subjects undergoing ACLR led to improved knee function based on the single-legged hop test and self-reported assessment using the modified Cincinnati score. These effects were sustained at 12 weeks postoperatively. This study supports prehabilitation as a consideration for patients awaiting ACLR; however, further studies are warranted.