Systematic identification of functional orthologs based on protein network comparison

Annotating protein function across species is an important task that is often complicated by the presence of large paralogous gene families. Here, we report a novel strategy for identifying functionally related proteins that supplements sequence-based comparisons with information on conserved protein-protein interactions. First, the protein interaction networks of two species are aligned by assigning proteins to sequence homology clusters using the Inparanoid algorithm. Next, probabilistic inference is performed on the aligned networks to identify pairs of proteins, one from each species, that are likely to retain the same function based on conservation of their interacting partners. Applying this method to Drosophila melanogaster and Saccharomyces cerevisiae, we analyze 121 cases for which functional orthology assignment is ambiguous when sequence similarity is used alone. In 61 of these cases, the network supports a different protein pair than that favored by sequence comparisons. These results suggest that network analysis can be used to provide a key source of information for refining sequence-based homology searches.     

Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana

Ionizing radiation has long been known to induce heritable mutagenic change in DNA sequence. However, the genome-wide effect of radiation is not well understood. Here we report the molecular properties and frequency of mutations in phenotypically selected mutant lines isolated following exposure of the genetic model flowering plant Arabidopsis thaliana to fast neutrons (FNs). Previous studies suggested that FNs predominantly induce deletions longer than a kilobase in A. thaliana. However, we found a higher frequency of single base substitution than deletion mutations. While the overall frequency and molecular spectrum of fast-neutron (FN)-induced single base substitutions differed substantially from those of "background" mutations arising spontaneously in laboratory-grown plants, G:C>A:T transitions were favored in both. We found that FN-induced G:C>A:T transitions were concentrated at pyrimidine dinucleotide sites, suggesting that FNs promote the formation of mutational covalent linkages between adjacent pyrimidine residues. In addition, we found that FNs induced more single base than large deletions, and that these single base deletions were possibly caused by replication slippage. Our observations provide an initial picture of the genome-wide molecular profile of mutations induced in A. thaliana by FN irradiation and are particularly informative of the nature and extent of genome-wide mutation in lines selected on the basis of mutant phenotypes from FN-mutagenized A. thaliana populations.     

Superparamagnetic iron oxide (SPIO) labeling efficiency and subsequent MRI tracking of native cell populations pertinent to pulmonary heart valve tissue engineering studies

The intimal and medial linings of the pulmonary artery consist largely of vascular endothelial cells (VECs) and vascular smooth muscle cells (VSMCs), respectively. The migration of these cell types to a potential tissue-engineered pulmonary valve (TEPV) implant process is therefore of interest in understanding the valve remodeling process. Visualization and cell tracking by MRI, which employs hypointense contrast achievable through the use of superparamagnetic iron oxide (SPIO) microparticles to label cells, provides a method in which this can be studied. We investigated the SPIO labeling efficiency of human VECs and VSMCs, and used two- and three-dimensional gradient echo sequences to track the migration of these cells in agar gel constructs. Protamine sulfate (4.5 μg/mL) was used to enhance SPIO uptake and was found to have no influence on cell viability or proliferation. MRI experiments were initially performed using a 9.4-T scanner. The results demonstrated that the spatial positions of hypointense spots were relatively unchanged over 12 days. Subsequent MR experiments performed at 7 T demonstrated that three-dimensional imaging provided the best spatial resolution to assess cell fate. R(2)* maps were bright in SPIO cell-encapsulated gels in comparison with unlabeled counterparts. Signal voids were ruled out as hypointense regions owing to the smooth exponential decay of T(2)* in these voxels. As a next step, we intend to use the SPIO cell labeling and MR protocols established in this study to assess whether hemodynamic stresses will alter the vascular cell migratory patterns. These studies will shed light on the mechanisms of vascular remodeling after TEPV implantation.     

The effect of cetylated fatty esters and physical therapy on myofascial pain syndrome of the neck

Participants with Myofascial Pain Syndrome (MPS) of the neck were randomly assigned into 2 groups of the double-blinded study: topical cetylated fatty ester complex (CFEC) cream application plus physical therapy (CF-PT; n=37), and placebo cream application plus physical therapy (PL-PT; n=35). There were 3 visits during 4 weeks of treatment. Physical Therapy (PT), given twice/week, included Ischaemic Compression, Deep Pressure Trigger Point Massage and Myofascial Releases. Topical cream [CFEC cream (5.6%) and 1.5% menthol] or placebo cream [1.5% menthol, in a cream base] was applied twice/day. CF-PT provided the fastest and most effective study treatment modality. The addition of CFEC cream to PT resulted in statistically significant improvements, compared to PL-PT, for reduction of pain, neck disability and life quality indicators. Our results indicate that cetylated derivatives of fatty acids can effectively reduce pain and symptoms associated with neck MPS, when combined with physical therapy.     

Workstyle Risk Factors for Work Related Musculoskeletal Symptoms Among Computer Professionals in India

Introduction Work-related musculoskeletal disorders are common in computer professionals. Workstyle may be one of the risk factors in the development of musculoskeletal discomfort. The objective of this retrospective study was to examine the prevalence of adverse workstyle in computer professionals from India and to evaluate if workstyle factors were predictors of pain and loss of productivity. Methods Office workers from various information technology (IT) companies in India responded to the short-form workstyle questionnaire and pain questionnaire. Correlation analyses were conducted to examine the associations between different variables followed by a multivariate logistic regression to understand the unique predictors of pain and loss of productivity. Results 4,500 participants responded to the workstyle and pain questionnaire. 22% of participants were reported to have a high risk of an adverse workstyle. 63% of participants reported pain symptoms. Social reactivity, lack of breaks, and deadlines/pressure subscales of workstyle questionnaire were significantly correlated with pain and loss of productivity. Regression analyses revealed that workstyle factors and duration of computer use per day were significant predictors of pain. Conclusion Workstyle seems to be a mediating factor for musculoskeletal pain, discomfort, and loss of productivity. Based on the study findings, it is recommended that intervention efforts directed towards prevention of musculoskeletal disorders should focus on psychosocial work factors such adverse workstyle in addition to biomechanical risk factors.