PDNAsite:identification of DNA-binding site from protein sequence by incorporating spatial and sequence context

Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. Most of the existing computational approaches employed only the sequence context of the target residue for its prediction. In the present study, for each target residue, we applied both the spatial context and the sequence context to construct the feature space. Subsequently, Latent Semantic Analysis (LSA) was applied to remove the redundancies in the feature space. Finally, a predictor (PDNAsite) was developed through the integration of the support vector machines (SVM) classifier and ensemble learning. Results on the PDNA-62 and the PDNA-224 datasets demonstrate that features extracted from spatial context provide more information than those from sequence context and the combination of them gives more performance gain. An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. The comparison between our proposed PDNAsite method and the existing methods indicate that PDNAsite outperforms most of the existing methods and is a useful tool for DNA-binding site identification. A web-server of our predictor (http://hlt.hitsz.edu.cn:8080/PDNAsite/) is made available for free public accessible to the biological research community

Energy compensation following consumption of sugar-reduced products: a randomized controlled trial

PURPOSE: Consumption of sugar-reformulated products (commercially available foods and beverages that have been reduced in sugar content through reformulation) is a potential strategy for lowering sugar intake at a population level. The impact of sugar-reformulated products on body weight, energy balance (EB) dynamics and cardiovascular disease risk indicators has yet to be established. The REFORMulated foods (REFORM) study examined the impact of an 8-week sugar-reformulated product exchange on body weight, EB dynamics, blood pressure, arterial stiffness, glycemia and lipemia. METHODS: A randomized, controlled, double-blind, crossover dietary intervention study was performed with fifty healthy normal to overweight men and women (age 32.0 ± 9.8 year, BMI 23.5 ± 3.0 kg/m2) who were randomly assigned to consume either regular sugar or sugar-reduced foods and beverages for 8 weeks, separated by 4-week washout period. Body weight, energy intake (EI), energy expenditure and vascular markers were assessed at baseline and after both interventions. RESULTS: We found that carbohydrate (P < 0.001), total sugars (P < 0.001) and non-milk extrinsic sugars (P < 0.001) (% EI) were lower, whereas fat (P = 0.001) and protein (P = 0.038) intakes (% EI) were higher on the sugar-reduced than the regular diet. No effects on body weight, blood pressure, arterial stiffness, fasting glycemia or lipemia were observed. CONCLUSIONS: Consumption of sugar-reduced products, as part of a blinded dietary exchange for an 8-week period, resulted in a significant reduction in sugar intake. Body weight did not change significantly, which we propose was due to energy compensation

Transcriptional landscape of bone marrow-derived very small embryonic-like stem cells during hypoxia

<p>Abstract</p> <p>Background</p> <p>Hypoxia is a ubiquitous feature of many lung diseases and elicits cell-specific responses. While the effects of hypoxia on stem cells have been examined under <it>in vitro </it>conditions, the consequences of <it>in vivo </it>oxygen deprivation have not been studied.</p> <p>Methods</p> <p>We investigated the effects of <it>in vivo </it>hypoxia on a recently characterized population of pluripotent stem cells known as very small embryonic-like stem cells (VSELs) by whole-genome expression profiling and measuring peripheral blood stem cell chemokine levels.</p> <p>Results</p> <p>We found that exposure to hypoxia in mice mobilized VSELs from the bone marrow to peripheral blood, and induced a distinct genome-wide transcriptional signature. Applying a computationally-intensive methodology, we identified a hypoxia-induced gene interaction network that was functionally enriched in a diverse array of programs including organ-specific development, stress response, and wound repair. Topographic analysis of the network highlighted a number of densely connected hubs that may represent key controllers of stem cell response during hypoxia and, therefore, serve as putative targets for altering the pathophysiologic consequences of hypoxic burden.</p> <p>Conclusions</p> <p>A brief exposure to hypoxia recruits pluripotent stem cells to the peripheral circulation and actives diverse transcriptional programs that are orchestrated by a selective number of key genes.</p

Oxford Phase 3 unicompartmental knee arthroplasty: medium-term results of a minimally invasive surgical procedure

PURPOSE: In the last decade, a major increase in the use of and interest in unicompartmental knee arthroplasty (UKA) has developed. The Oxford Phase 3 UKA is implanted with a minimally invasive technique using newly developed instruments. The objective of this prospective study was to evaluate the outcome of UKA in patients with medial osteoarthritis of the knee in a high-volume unit. METHODS: Two-hundred and forty-four UKAs were performed with a minimally invasive approach. The median age was 72 (43-91) years. The median follow-up was 4.2 years (range 1-10.4 years). Fourteen patients died, and nine were considered to be lost to follow-up, but all had a well-functioning prosthesis in situ until their last follow-up. Pain, function and health-related quality of life were evaluated pre- and postoperatively using patient- and assessor-based outcome scores, as well as radiographic evidence. RESULTS: The mean Knee Society knee and function scores, WOMAC-scores, Oxford-score and VAS pain and satisfaction all improved. Nine knees required revision. Eleven patients required an additional arthroscopic procedure due to persisting pain secondary to intra-articular pathology, and four patients required manipulation under anaesthesia because of limited range of motion. The 7-year cumulative survival rate of the arthroplasty was 94.4%. A low incidence (21%) of a radiolucent line beneath the tibial component was observed at 5 years of follow-up. CONCLUSION: This study showed a high survival rate of the Oxford Phase 3 UKA. Patient satisfaction and functional performance were also very high. Major complication rate was low; in addition, the incidence of radiolucency under the tibial component, when compared to present literature, was low. When strict indication criteria are followed, excellent, durable, and in our opinion reliable, results can be expected for this procedur

The NSL Complex Regulates Housekeeping Genes in Drosophila

MOF is the major histone H4 lysine 16-specific (H4K16) acetyltransferase in mammals and Drosophila. In flies, it is involved in the regulation of X-chromosomal and autosomal genes as part of the MSL and the NSL complexes, respectively. While the function of the MSL complex as a dosage compensation regulator is fairly well understood, the role of the NSL complex in gene regulation is still poorly characterized. Here we report a comprehensive ChIP–seq analysis of four NSL complex members (NSL1, NSL3, MBD-R2, and MCRS2) throughout the Drosophila melanogaster genome. Strikingly, the majority (85.5%) of NSL-bound genes are constitutively expressed across different cell types. We find that an increased abundance of the histone modifications H4K16ac, H3K4me2, H3K4me3, and H3K9ac in gene promoter regions is characteristic of NSL-targeted genes. Furthermore, we show that these genes have a well-defined nucleosome free region and broad transcription initiation patterns. Finally, by performing ChIP–seq analyses of RNA polymerase II (Pol II) in NSL1- and NSL3-depleted cells, we demonstrate that both NSL proteins are required for efficient recruitment of Pol II to NSL target gene promoters. The observed Pol II reduction coincides with compromised binding of TBP and TFIIB to target promoters, indicating that the NSL complex is required for optimal recruitment of the pre-initiation complex on target genes. Moreover, genes that undergo the most dramatic loss of Pol II upon NSL knockdowns tend to be enriched in DNA Replication–related Element (DRE). Taken together, our findings show that the MOF-containing NSL complex acts as a major regulator of housekeeping genes in flies by modulating initiation of Pol II transcription

The three in one procedure: how I do it.

Recurrent patella dislocation is common, and selection of an appropriate stabilisation procedure is important for a successful outcome. We describe a combined proximal and distal realignment procedure to adjust soft tissue tension around the patella. This procedure, the 'Three in One' involves a combination of a lateral release, vastus medialis obliquus muscle advancement, and transfer of the medial third of the patellar tendon to the medial collateral ligament. This is a safe, reliable procedure for patients with recurrent dislocation of the patella resulting from an imbalance of soft tissue tension around the patella, but with a normally sited patella and normal trochlea

Selective Kirschner wiring for displaced distal radial fractures in children.

OBJECTIVES: This study was designed to evaluate our departmental policy of plaster immobilization and selective Kirschner (K) wiring for the management of displaced distal radius fractures in children. METHODS: On a retrospective basis, we evaluated a consecutive series of 112 childhood displaced distal radius fractures (108 patients; 77 boys, 31 girls; mean age 10.5+/-2.6 years; range 5 to 16 years) presenting with clinical deformity during a two-year period. There were 97 incompletely displaced (86.6%), and 15 completely displaced (13.4%) fractures. All the fractures were managed with manipulation under general anesthesia and plaster immobilization. Additionally, K-wire fixation was performed following manipulation in seven (46.7%) of the completely displaced fractures. The mean follow-up period was 1.1 years (range 10 weeks to 2 years). RESULTS: The mean angulation of fractures prior to manipulation was 21.5+/-10.1 degrees, it decreased to 2.4+/-4.8 degrees following manipulation. Remanipulation was required in 11 fractures (9.8%) based on clinical and radiographic findings of redisplacement. Of these, eight fractures (8.3%) were incompletely displaced, and three fractures (20%) were completely displaced. All completely displaced fractures that required remanipulation had been additionally treated with K-wire fixation. Fractures requiring further treatment had a mean angulation of 17.1+/-5.8 degrees prior to remanipulation, and a mean residual angulation of 4.7+/-6.0 degrees at final radiographic assessment. A perfect fracture reduction was achieved in all the patients with a Salter-Harris II injury (n=22), and none of these patients required remanipulation. However, the quality of initial reduction was not associated with the development of redisplacement. There was no significant difference between isolated distal radius fractures (n=58) and combined radius and ulna fractures (n=32) with respect to remanipulation rate and final angulation (p>0.05). Final radiographs showed a significantly greater angulation in fractures which were initially completely displaced in comparison with those that were incompletely displaced (8.2+/-7.1 degrees vs. 4.2+/-5.7 degrees; p=0.024), but this was not of clinical significance. None of the patients had radial shortening and no K-wire related complications were encountered. CONCLUSION: Our data suggest that there should be other factors involved in the development of redisplacement and the need for remanipulation other than the degree of fracture displacement and the quality of initial reduction. Selective K-wire fixation in displaced fractures does not seem to decrease redisplacement and remanipulation rates