RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs

Structural characteristics are essential for the functioning of many noncoding RNAs and cis‐regulatory elements of mRNAs. SNPs may disrupt these structures, interfere with their molecular function, and hence cause a phenotypic effect. RNA folding algorithms can provide detailed insights into structural effects of SNPs. The global measures employed so far suffer from limited accuracy of folding programs on large RNAs and are computationally too demanding for genome‐wide applications. Here, we present a strategy that focuses on the local regions of maximal structural change between mutant and wild‐type. These local regions are approximated in a “screening mode” that is intended for genome‐wide applications. Furthermore, localized regions are identified as those with maximal discrepancy. The mutation effects are quantified in terms of empirical P values. To this end, the RNAsnp software uses extensive precomputed tables of the distribution of SNP effects as function of length and GC content. RNAsnp thus achieves both a noise reduction and speed‐up of several orders of magnitude over shuffling‐based approaches. On a data set comprising 501 SNPs associated with human‐inherited diseases, we predict 54 to have significant local structural effect in the untranslated region of mRNAs. RNAsnp is available at http://rth.dk/resources/rnasnp .     

Resistance training decreases matrix metalloproteinase-2 activity in quadriceps tendon in a rat model of osteoarthritis

BackgroundOsteoarthritis (OA) is a degenerative disease that induces peri-articular tissue degradation. OA induces an imbalance between synthesis and degradation of the extracellular matrix components in favor of catabolic events, promoting pathological remodeling and involving degradative enzymes, such as matrix metalloproteinases (MMPs).ObjectiveThis study aimed to investigate the effects of 8-weeks resistance training (RT) on MMP-2 activity in the quadriceps tendon and patellar tendon in an OA model.MethodsTwenty-four Wistar rats were randomly divided into six groups: Control, Exercise, Sham, Sham with Exercise, OA, and OA with Exercise (OAE). The OA model was performed by anterior cruciate ligament transection surgery on the left knee. The 8-week RT consisted of climbing a 1.1-m vertical ladder three times per week with progressive weights secured to the animals’ tails. MMP-2 activity was analyzed by zymography.ResultsThe OAE group displayed lower pro, intermediate, and active MMP-2 activity in the quadriceps tendon compared with the OA group (p < 0.05). For the patellar tendon, there was no significant difference between the OAE group compared with the other groups (p > 0.05) for pro, intermediate, and active MMP-2 activity. Moreover, MMP-2 activity differed between tissues, the OA and OAE groups presented lower pro, intermediate, and active MMP-2 activity in the quadriceps tendon compared to the patellar tendon.ConclusionRT induced down-regulated MMP-2 activity in the quadriceps tendon. RT is a potential therapeutic approach to minimize the deleterious effects of extracellular matrix degeneration.     

Associations of 25‐Hydroxyvitamin D and 1,25‐Dihydroxyvitamin D With Bone Mineral Density,Bone Mineral Density Change,and Incident Nonvertebral Fracture

Relationships between 1,25‐dihydroxyvitamin D (1,25(OH)₂D) and skeletal outcomes are uncertain. We examined the associations of 1,25(OH)₂D with bone mineral density (BMD), BMD change, and incident non‐vertebral fractures in a cohort of older men and compared them with those of 25‐hydroxyvitamin D (25OHD). The study population included 1000 men (aged 74.6 ± 6.2 years) in the Osteoporotic Fractures in Men (MrOS) study, of which 537 men had longitudinal dual‐energy X‐ray absorptiometry (DXA) data (4.5 years of follow‐up). A case‐cohort design and Cox proportional hazards models were used to test the association between vitamin D metabolite levels and incident nonvertebral and hip fractures. Linear regression models were used to estimate the association between vitamin D measures and baseline BMD and BMD change. Interactions between 25OHD and 1,25(OH)₂D were tested for each outcome. Over an average follow‐up of 5.1 years, 432 men experienced incident nonvertebral fractures, including 81 hip fractures. Higher 25OHD was associated with higher baseline BMD, slower BMD loss, and lower hip fracture risk. Conversely, men with higher 1,25(OH)₂D had lower baseline BMD. 1,25(OH)₂D was not associated with BMD loss or nonvertebral fracture. Compared with higher levels of calcitriol, the risk of hip fracture was higher in men with the lowest 1,25(OH)₂D levels (8.70 to 51.60 pg/mL) after adjustment for baseline hip BMD (hazard ratio [HR] = 1.99, 95% confidence interval [CI] 1.19–3.33). Adjustment of 1,25(OH)₂D data for 25OHD (and vice versa) had little effect on the associations observed but did attenuate the hip fracture association of both vitamin D metabolites. In older men, higher 1,25(OH)₂D was associated with lower baseline BMD but was not related to the rate of bone loss or nonvertebral fracture risk. However, with BMD adjustment, a protective association for hip fracture was found with higher 1,25(OH)₂D. The associations of 25OHD with skeletal outcomes were generally stronger than those for 1,25(OH)₂D. These results do not support the hypothesis that measures of 1,25(OH)₂D improve the ability to predict adverse skeletal outcomes when 25OHD measures are available. © 2015 American Society for Bone and Mineral Research.     

A new strategy for label-free detection of lymphoma cancer cells

In this paper, a new strategy for highly selective and sensitive direct detection of lymphoma cells by exploiting the interaction between a peptide and its B-cell receptor, has been evaluated. In particular, an idiotype peptide, able to specifically bind the B-cell receptor of A20 cells in mice engrafted with A20 lymphoma, has been used as molecular probe. The new detection technique has been demonstrated on a planar crystalline silicon chip. Coverage of 85% of silicon surface and detection efficiency of 8.5 × 10⁻³ cells/μm² were obtained. The recognition strategy promises to extend its application in studying the interaction between ligands and their cell-surface receptors.OCIS codes: (000.1430) Biology and medicine, (280.1415) Biological sensing and sensors     

Novel treatment of ovarian cancer cell lines with Imatinib mesylate combined with Paclitaxel and Carboplatin leads to receptor-mediated antiproliferative effects

Purpose  Imatinib is a small molecule inhibiting the tyrosine kinases bcr-abl, c-kit, PDGFR-α and PDGFR-β. Investigations were performed to screen ovarian cancer cell lines and tumor samples for target receptor expression. Effects of Imatinib on cell proliferation and apoptosis induction were measured with and without additional cytotoxic agents. Methods  Expression patterns of abl, c-kit, PDGFR-α and PDGFR-β (Imatinib targets) were studied in 5 cell lines and 111 tissue arrays by PCR and immunohistochemistry. Proliferation assays were performed with single agent Imatinib or combined with Paclitaxel and Carboplatin. Apoptosis was measured by DNA fragmentation. Results  All cell lines expressed abl and PDGFR-β. C-kit was only expressed in 2/5 cell lines and PDGFR-α in 4/5. Imatinib reduced cell growth and lead to pro-apoptotic changes. Combination of Carboplatin, Paclitaxel and Imatinib showed synergistic activity. Conclusions  Our results suggest that Imatinib may be useful for the specific treatment of ovarian cancer as an add-on to conventional chemotherapy. C. Mundhenke and M. T. Weigel contributed equally to this work.     

Stimulus features coded by single neurons of a macaque body category selective patch

Body category-selective regions of the primate temporal cortex respond to images of bodies, but it is unclear which fragments of such images drive single neurons’ responses in these regions. Here we applied the Bubbles technique to the responses of single macaque middle superior temporal sulcus (midSTS) body patch neurons to reveal the image fragments the neurons respond to. We found that local image fragments such as extremities (limbs), curved boundaries, and parts of the torso drove the large majority of neurons. Bubbles revealed the whole body in only a few neurons. Neurons coded the features in a manner that was tolerant to translation and scale changes. Most image fragments were excitatory but for a few neurons both inhibitory and excitatory fragments (opponent coding) were present in the same image. The fragments we reveal here in the body patch with Bubbles differ from those suggested in previous studies of face-selective neurons in face patches. Together, our data indicate that the majority of body patch neurons respond to local image fragments that occur frequently, but not exclusively, in bodies, with a coding that is tolerant to translation and scale. Overall, the data suggest that the body category selectivity of the midSTS body patch depends more on the feature statistics of bodies (e.g., extensions occur more frequently in bodies) than on semantics (bodies as an abstract category).The body category-selective regions in the human occipito-temporal cortex are defined as those that respond to images of bodies (1–8). We previously identified two bilateral regions in the macaque inferotemporal cortex that respond stronger to monkey, human, and animal bodies in comparison with other stimuli, including faces (6). Subsequent single-unit recordings in the posterior body patch [i.e., the middle superior temporal sulcus (midSTS) body patch] demonstrated that indeed the average spiking activity of the neuron population was greater to images of bodies compared with other objects. However, the responses of single neurons showed a strong selectivity for particular body—and sometimes nonbody—images (7). However, it is still unknown what particular stimulus features single body patch neurons respond to. Moreover, we still do not know how those neurons code information about different animate and inanimate stimuli.The Bubbles technique (9), in which parts of the image of an object are sampled by trial-unique randomly positioned Gaussian apertures, has been used successfully in many psychophysical studies to reveal the features critical for certain perceptual tasks such as face identification, gender discrimination, emotional discrimination, and so forth (e.g., refs. 9–13). Although this technique has been used in neuroimaging [functional MRI (fMRI), EEG, magnetoencephalography (MEG), and electrocorticography] studies (11, 12, 14), it has rarely been exploited in single-unit studies (15, 16), and this only for face stimuli.Here, we used the Bubbles technique to reveal the image fragments that drive single midSTS body patch neurons. Bubbles provides an unbiased method for sampling the images with the advantage that it requires no prior specification of stimulus features to which the neurons are supposed to be selective. With fMRI, we first defined the midSTS body patch in two monkeys. Then, in this identified body patch we recorded the spiking activity of well-isolated single neurons in response to 100 images of various categories. Based on the spiking activity to the 100 images, we selected for each neuron a response-eliciting image. Then, we sampled the selected image at five different spatial scales with randomly positioned Gaussian apertures and recorded the responses of the neuron to a large number of these trial-unique Bubbles stimuli. Following the experiment, we applied reverse correlation to relate the excitatory and inhibitory neural responses to particular image fragments.Furthermore, we assessed whether the revealed image fragments tolerated changes in spatial location and size of the Bubbles stimuli or instead reflected spatially localized image regions. We showed before that many midSTS body patch neurons respond to silhouettes of bodies (17). Silhouettes isolate shape contours, removing texture and shading information. Thus, in a subset of neurons, we applied Bubbles to a silhouette version of the selected image.