NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops

In a combined NMR/MD study, the temperature-dependent changes in the conformation of two members of the RNA YNMG-tetraloop motif (cUUCGg and uCACGg) have been investigated at temperatures of 298, 317 and 325 K. The two members have considerable different thermal stability and biological functions. In order to address these differences, the combined NMR/MD study was performed. The large temperature range represents a challenge for both, NMR relaxation analysis (consistent choice of effective bond length and CSA parameter) and all-atom MD simulation with explicit solvent (necessity to rescale the temperature). A convincing agreement of experiment and theory is found. Employing a principle component analysis of the MD trajectories, the conformational distribution of both hairpins at various temperatures is investigated. The ground state conformation and dynamics of the two tetraloops are indeed found to be very similar. Furthermore, both systems are initially destabilized by a loss of the stacking interactions between the first and the third nucleobase in the loop region. While the global fold is still preserved, this initiation of unfolding is already observed at 317 K for the uCACGg hairpin but at a significantly higher temperature for the cUUCGg hairpin

A new interdisciplinary treatment strategy versus usual medical care for the treatment of subacromial impingement syndrome: a randomized controlled trial

BACKGROUND: Subacromial impingement syndrome (SIS) is the most frequently recorded shoulder disorder. When conservative treatment of SIS fails, a subacromial decompression is warranted. However, the best moment of referral for surgery is not well defined. Both early and late referrals have disadvantages – unnecessary operations and smaller improvements in shoulder function, respectively. This paper describes the design of a new interdisciplinary treatment strategy for SIS (TRANSIT), which comprises rules to treat SIS in primary care and a well-defined moment of referral for surgery. METHODS/DESIGN: The effectiveness of an arthroscopic subacromial decompression versus usual medical care will be evaluated in a randomized controlled trial (RCT). Patients are eligible for inclusion when experiencing a recurrence of SIS within one year after a first episode of SIS which was successfully treated with a subacromial corticosteroid injection. After inclusion they will receive injection treatment again by their general practitioner. When, after this treatment, there is a second recurrence within a year post-injection, the participants will be randomized to either an arthroscopic subacromial decompression (intervention group) or continuation of usual medical care (control group). The latter will be performed by a general practitioner according to the Dutch National Guidelines for Shoulder Problems. At inclusion, at randomization and three, six and 12 months post-randomization an outcome assessment will take place. The primary outcome measure is the patient-reported Shoulder Disability Questionnaire. The secondary outcome measures include both disease-specific and generic measures, and an economic evaluation. Treatment effects will be compared for all measurement points by using a GLM repeated measures analyses. DISCUSSION: The rationale and design of an RCT comparing arthroscopic subacromial decompression with usual medical care for subacromial impingement syndrome are presented. The results of this study will improve insight into the best moment of referral for surgery for SIS

Cholesteryl Ester Transfer Protein (CETP) Polymorphisms Affect mRNA Splicing, HDL Levels, and Sex-Dependent Cardiovascular Risk

Polymorphisms in and around the Cholesteryl Ester Transfer Protein (CETP) gene have been associated with HDL levels, risk for coronary artery disease (CAD), and response to therapy. The mechanism of action of these polymorphisms has yet to be defined. We used mRNA allelic expression and splice isoform measurements in human liver tissues to identify the genetic variants affecting CETP levels. Allelic CETP mRNA expression ratios in 56 human livers were strongly associated with several variants 2.5–7 kb upstream of the transcription start site (e.g., rs247616 p = 6.4×10−5, allele frequency 33%). In addition, a common alternatively spliced CETP isoform lacking exon 9 (Δ9), has been shown to prevent CETP secretion in a dominant-negative manner. The Δ 9 expression ranged from 10 to 48% of total CETP mRNA in 94 livers. Increased formation of this isoform was exclusively associated with an exon 9 polymorphism rs5883-C>T (p = 6.8×10−10) and intron 8 polymorphism rs9930761-T>C (5.6×10−8) (in high linkage disequilibrium with allele frequencies 6–7%). rs9930761 changes a key splicing branch point nucleotide in intron 8, while rs5883 alters an exonic splicing enhancer sequence in exon 9

Evidence-Based Annotation of the Malaria Parasite's Genome Using Comparative Expression Profiling

A fundamental problem in systems biology and whole genome sequence analysis is how to infer functions for the many uncharacterized proteins that are identified, whether they are conserved across organisms of different phyla or are phylum-specific. This problem is especially acute in pathogens, such as malaria parasites, where genetic and biochemical investigations are likely to be more difficult. Here we perform comparative expression analysis on Plasmodium parasite life cycle data derived from P. falciparum blood, sporozoite, zygote and ookinete stages, and P. yoelii mosquito oocyst and salivary gland sporozoites, blood and liver stages and show that type II fatty acid biosynthesis genes are upregulated in liver and insect stages relative to asexual blood stages. We also show that some universally uncharacterized genes with orthologs in Plasmodium species, Saccharomyces cerevisiae and humans show coordinated transcription patterns in large collections of human and yeast expression data and that the function of the uncharacterized genes can sometimes be predicted based on the expression patterns across these diverse organisms. We also use a comprehensive and unbiased literature mining method to predict which uncharacterized parasite-specific genes are likely to have roles in processes such as gliding motility, host-cell interactions, sporozoite stage, or rhoptry function. These analyses, together with protein-protein interaction data, provide probabilistic models that predict the function of 926 uncharacterized malaria genes and also suggest that malaria parasites may provide a simple model system for the study of some human processes. These data also provide a foundation for further studies of transcriptional regulation in malaria parasites

Dietary factors impact on the association between CTSS variants and obesity related traits.

Cathepsin S, a protein coded by the CTSS gene, is implicated in adipose tissue biology--this protein enhances adipose tissue development. Our hypothesis is that common variants in CTSS play a role in body weight regulation and in the development of obesity and that these effects are influenced by dietary factors--increased by high protein, glycemic index and energy diets

Evolutionary significance of inversions in legume chloroplast DNAs

Cloned genes from tobacco, spinach, and pea were used as hybridization probes to localize 36 protein genes on the chloroplast chromosomes of four legumes — mung bean, common bean, soybean, and pea. The first three chloroplast DNAs (cpDNAs), all of which retain a large inverted repeat, have an identical gene order with but one exception. A 78 kb segment encompassing nearly the entire large single copy region is inverted in mung bean and common bean relative to soybean and non-legumes. The simplest evolutionary explanation for this difference is a 78 kb inversion, with one endpoint between rps8 and inf A and the second between psb A and rpl2 . However, we can not rule out a two-step re-arrangement (consisting of successive expansion and contraction of the inverted repeat) leading to the relocation of a block of six ribosomal protein genes ( rps 19- rps 8) from one end of the large single copy region to the other. Analysis of gene locations in pea cpDNA, which lacks the large inverted repeat, combined with cross-hybridization studies using 59 clones covering the mung bean genome, leads to a refined picture of the position and nature of the numerous rearrangements previously described in the pea genome. A minimum of eight large inversions are postulated to account for these rearrangements. None of these inversions disrupt groups of genes that are transcriptionally linked in angiosperm cpDNA. Rather, the end-points of inversions are associated with relatively spacer-rich segments of the genome, many of which contain tRNA genes. All of the pea-specific inversions are shown to be positionally distinct from those recently described in a closely related legume, broad bean.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46965/1/294_2004_Article_BF00405856.pd

Properties and customization of sensor materials for biomedical applications.

Low-power chemo- and biosensing devices capable of monitoring clinically important parameters in real time represent a great challenge in the analytical field as the issue of sensor calibration pertaining to keeping the response within an accurate calibration domain is particularly significant (1–4). Diagnostics, personal health, and related costs will also benefit from the introduction of sensors technology (5–7). In addition, with the introduction of Registration, Evaluation, Authorization, and Restriction of Chemical Substances (REACH) regulation, unraveling the cause–effect relationships in epidemiology studies will be of outmost importance to help establish reliable environmental policies aimed at protecting the health of individuals and communities (8–10). For instance, the effect of low concentration of toxic elements is seldom investigated as physicians do not have means to access the data (11)

Management of nystagmus in children: A review of the literature and current practice in UK specialist services

Nystagmus is an eye movement disorder characterised by abnormal, involuntary rhythmic oscillations of one or both eyes, initiated by a slow phase. It is not uncommon in the UK and regularly seen in paediatric ophthalmology and adult general/strabismus clinics. In some cases, it occurs in isolation, and in others, it occurs as part of a multisystem disorder, severe visual impairment or neurological disorder. Similarly, in some cases, visual acuity can be normal and in others can be severely degraded. Furthermore, the impact on vision goes well beyond static acuity alone, is rarely measured and may vary on a minute-to-minute, day-to-day or month-to-month basis. For these reasons, management of children with nystagmus in the UK is varied, and patients report hugely different experiences and investigations. In this review, we hope to shine a light on the current management of children with nystagmus across five specialist centres in the UK in order to present, for the first time, a consensus on investigation and clinical management

Accelerating functional gene discovery in osteoarthritis

Osteoarthritis causes debilitating pain and disability, resulting in a considerable socioeconomic burden, yet no drugs are available that prevent disease onset or progression. Here, we develop, validate and use rapid-throughput imaging techniques to identify abnormal joint phenotypes in randomly selected mutant mice generated by the International Knockout Mouse Consortium. We identify 14 genes with functional involvement in osteoarthritis pathogenesis, including the homeobox gene Pitx1, and functionally characterize 6 candidate human osteoarthritis genes in mouse models. We demonstrate sensitivity of the methods by identifying age-related degenerative joint damage in wild-type mice. Finally, we phenotype previously generated mutant mice with an osteoarthritis-associated polymorphism in the Dio2 gene by CRISPR/Cas9 genome editing and demonstrate a protective role in disease onset with public health implications. We hope this expanding resource of mutant mice will accelerate functional gene discovery in osteoarthritis and offer drug discovery opportunities for this common, incapacitating chronic disease