Overlapping Antisense Transcription in the Human Genome

Accumulating evidence indicates an important role for non-coding RNA molecules in eukaryotic cell regulation. A small number of coding and non-coding overlapping antisense transcripts (OATs) in eukaryotes have been reported, some of which regulate expression of the corresponding sense transcript. The prevalence of this phenomenon is unknown, but there may be an enrichment of such transcripts at imprinted gene loci. Taking a bioinformatics approach, we systematically searched a human mRNA database (RefSeq) for complementary regions that might facilitate pairing with other transcripts. We report 56 pairs of overlapping transcripts, in which each member of the pair is transcribed from the same locus. This allows us to make an estimate of 1000 for the minimum number of such transcript pairs in the entire human genome. This is a surprisingly large number of overlapping gene pairs and, clearly, some of the overlaps may not be functionally significant. Nonetheless, this may indicate an important general role for overlapping antisense control in gene regulation. EST databases were also investigated in order to address the prevalence of cases of imprinted genes with associated non-coding overlapping, antisense transcripts. However, EST databases were found to be completely inappropriate for this purpose

Proximity to Sports Facilities and Sports Participation for Adolescents in Germany

Objectives - To assess the relationship between proximity to specific sports facilities and participation in the corresponding sports activities for adolescents in Germany. Methods - A sample of 1,768 adolescents aged 11–17 years old and living in 161 German communities was examined. Distances to the nearest sports facilities were calculated as an indicator of proximity to sports facilities using Geographic Information Systems (GIS). Participation in specific leisure-time sports activities in sports clubs was assessed using a self-report questionnaire and individual-level socio-demographic variables were derived from a parent questionnaire. Community-level socio-demographics as covariates were selected from the INKAR database, in particular from indicators and maps on land development. Logistic regression analyses were conducted to examine associations between proximity to the nearest sports facilities and participation in the corresponding sports activities. Results - The logisitic regression analyses showed that girls residing longer distances from the nearest gym were less likely to engage in indoor sports activities; a significant interaction between distances to gyms and level of urbanization was identified. Decomposition of the interaction term showed that for adolescent girls living in rural areas participation in indoor sports activities was positively associated with gym proximity. Proximity to tennis courts and indoor pools was not associated with participation in tennis or water sports, respectively. Conclusions - Improved proximity to gyms is likely to be more important for female adolescents living in rural areas

Variety of transversus thoracis muscle in relation to the internal thoracic artery: an autopsy study of 120 subjects

<p>Abstract</p> <p>Background</p> <p>The transversus thoracis muscle is a thin muscular layer on the inner surface of the anterior thoracic wall that is always in concern during harvesting of the internal thoracic artery. Because the muscle is poorly described in the surgical literature, the aim of the present study is to examine in details its variations.</p> <p>Methods</p> <p>The data was obtained at standard autopsies of 120 Caucasian subjects (Bulgarians) of both sexes (97 males and 23 females), ranging in age from 18 to 91 years (mean age 52.8 ± 17.8 years). The transversus thoracis morphology was thoroughly examined on the inner surface of the chest plates collected after routine incisions.</p> <p>Results</p> <p>An overall examination revealed that in majority of cases the transversus thoracis slips formed a complete muscular layer (left - 75.8%, right - 83.3%) or some of the slips (left - 22.5%, right - 15%) or all of them (left - 1.7%, right - 1.7%) were quite separated. Rarely (left - 3.3%, right - 5.8%), some fibrous slips of the transversus thoracis were noted. In 55.8% of the cases there was left/right muscle symmetry; 44.2% of the muscles were asymmetrical. Most commonly, the highest muscle attachment was to the second (left - 53.3%, right - 37.5%) or third rib (left - 29.2%, right - 46.7%). The sixth rib was the most common lowest attachment (left - 94.2%, right - 89.2%). Most frequently, the muscle was composed of four (left - 31.7%, right - 44.2%) or fifth slips (left - 53.3%, right - 40.8%).</p> <p>Conclusions</p> <p>This study provides detailed basic information on the variety of the transversus thoracic muscle. It also defines the range of the clearly visible, uncovered by the muscle part of the internal thoracic artery and the completeness of the muscular layer over it. The knowledge of these peculiar muscle-arterial relations would definitely be beneficial to cardiac surgeon in performing fast and safe arterial harvesting.</p

Embodying compassion: A virtual reality paradigm for overcoming excessive self-criticism

Virtual reality has been successfully used to study and treat psychological disorders such as phobias and posttraumatic stress disorder but has rarely been applied to clinically-relevant emotions other than fear and anxiety. Self-criticism is a ubiquitous feature of psychopathology and can be treated by increasing levels of self-compassion. We exploited the known effects of identification with a virtual body to arrange for healthy female volunteers high in self-criticism to experience self-compassion from an embodied first-person perspective within immersive virtual reality. Whereas observation and practice of compassionate responses reduced self-criticism, the additional experience of embodiment also increased self-compassion and feelings of being safe. The results suggest potential new uses for immersive virtual reality in a range of clinical conditions.N/

An optimized protocol for microarray validation by quantitative PCR using amplified amino allyl labeled RNA

<p>Abstract</p> <p>Background</p> <p>Validation of microarrays data by quantitative real-time PCR (qPCR) is often limited by the low amount of available RNA. This raised the possibility to perform validation experiments on the amplified amino allyl labeled RNA (AA-aRNA) leftover from microarrays. To test this possibility, we used an ongoing study of our laboratory aiming at identifying new biomarkers of graft rejection by the transcriptomic analysis of blood cells from brain-dead organ donors.</p> <p>Results</p> <p>qPCR for ACTB performed on AA-aRNA from 15 donors provided Cq values 8 cycles higher than when original RNA was used (P < 0.001), suggesting a strong inhibition of qPCR performed on AA-aRNA. When expression levels of 5 other genes were measured in AA-aRNA generated from a universal reference RNA, qPCR sensitivity and efficiency were decreased. This prevented the quantification of one low-abundant gene, which was readily quantified in un-amplified and un-labeled RNA. To overcome this limitation, we modified the reverse transcription (RT) protocol that generates cDNA from AA-aRNA as follows: addition of a denaturation step and 2-min incubation at room temperature to improve random primers annealing, a transcription initiation step to improve RT, and a final treatment with RNase H to degrade remaining RNA. Tested on universal reference AA-aRNA, these modifications provided a gain of 3.4 Cq (average from 5 genes, P < 0.001) and an increase of qPCR efficiency (from -1.96 to -2.88; P = 0.02). They also allowed for the detection of a low-abundant gene that was previously undetectable. Tested on AA-aRNA from 15 brain-dead organ donors, RT optimization provided a gain of 2.7 cycles (average from 7 genes, P = 0.004). Finally, qPCR results significantly correlated with microarrays.</p> <p>Conclusion</p> <p>We present here an optimized RT protocol for validation of microarrays by qPCR from AA-aRNA. This is particularly valuable in experiments where limited amount of RNA is available.</p

Search for Kaluza-Klein Graviton Emission in ppˉp\bar{p} Collisions at s=1.8\sqrt{s}=1.8 TeV using the Missing Energy Signature

We report on a search for direct Kaluza-Klein graviton production in a data sample of 84 ${pb}^{-1}$ of \ppb collisions at $\sqrt{s}$ = 1.8 TeV, recorded by the Collider Detector at Fermilab. We investigate the final state of large missing transverse energy and one or two high energy jets. We compare the data with the predictions from a $3+1+n$-dimensional Kaluza-Klein scenario in which gravity becomes strong at the TeV scale. At 95% confidence level (C.L.) for $n$=2, 4, and 6 we exclude an effective Planck scale below 1.0, 0.77, and 0.71 TeV, respectively.Comment: Submitted to PRL, 7 pages 4 figures/Revision includes 5 figure

Measurement of the average time-integrated mixing probability of b-flavored hadrons produced at the Tevatron

We have measured the number of like-sign (LS) and opposite-sign (OS) lepton pairs arising from double semileptonic decays of $b$ and $\bar{b}$-hadrons, pair-produced at the Fermilab Tevatron collider. The data samples were collected with the Collider Detector at Fermilab (CDF) during the 1992-1995 collider run by triggering on the existence of $\mu \mu$ and $e \mu$ candidates in an event. The observed ratio of LS to OS dileptons leads to a measurement of the average time-integrated mixing probability of all produced $b$-flavored hadrons which decay weakly, $\bar{\chi} = 0.152 \pm 0.007$ (stat.) $\pm 0.011$ (syst.), that is significantly larger than the world average $\bar{\chi} = 0.118 \pm 0.005$.Comment: 47 pages, 10 figures, 15 tables Submitted to Phys. Rev.

Leaf photosynthesis and associations with grain yield, biomass and nitrogen-use efficiency in landraces, synthetic-derived lines and cultivars in wheat

Future genetic progress in wheat grain yield will depend on increasing above-ground biomass and this must be achieved without commensurate increases in N fertilizer inputs to minimise environmental impacts. Our objective was to quantify variation in grain yield, above-ground biomass and N-use efficiency (NUE) and associated traits in a panel of diverse hexaploid wheat germplasm comprising: (i) landraces from the AE Watkins collection, (ii) synthetic-derived hexaploid lines in a cv. Paragon spring wheat background and (iii) UK modern cultivars including cv. Paragon under low N and high N conditions. A field experiment was carried out in two seasons examining 15 genotypes (five landraces, five synthetic-derived (SD) hexaploid lines and five UK modern cultivars) under low N and high N conditions at Nottingham University farm, UK. Machine-harvested grain yield, above-ground biomass and NUE were measured. Physiological traits were assessed including flag-leaf light-saturated photosynthetic rate (Amax) and relative chlorophyll content (SPAD) under HN conditions; and flag-leaf senescence duration and rate and Normalized Difference Vegetative Index (NDVI) under LN and HN conditions. Under HN conditions, the modern cultivars overall produced higher grain yield than the SD lines (+9.7%) and the landraces (+60.4%); and the modern cultivars and SD lines also produced higher biomass than the landraces (30.3% and 28.4%, respectively). Under LN conditions, reduction in grain yield and biomass compared to HN conditions was least for the landraces (−1% and −8.6%, respectively), intermediate for the SD lines (−7.4 and −10.2%, respectively) and highest for the modern cultivars (−9.3 and −24.6%, respectively). As a result, the SD lines had higher biomass (+17%) than the modern cultivars under LN conditions. Under HN conditions the synthetic derivatives (23.8 μmol m−2 s−1) and modern cultivars (241.1 μmol m−2 s−1) had higher pre-anthesis Amax than the landraces (19.7 μmol m−2 s−1) (P < 0.001). Pre-anthesis Amax was strongly positively linearly associated with above-ground biomass (R2 = 0.63, P < 0.001) and grain yield (R2 = 0.75, P < 0.001) amongst the 15 genotypes. Flag-leaf Amax was also positively linearly associated with flag-leaf relative chlorophyll content at anthesis (R2 = 0.74; P < 0.001). Comparing the SD lines to the recurrent parent Paragon, under HN conditions one line (SD 22) had higher pre-anthesis flag-leaf Amax than Paragon (P < 0.05). Under LN conditions one line (SD 24, +27%) had higher yield than Paragon (P < 0.05) and two lines (SD 24 and SD 38, +32% and +31%, respectively) had more biomass than Paragon (P < 0.05). Our results indicated that introgressing traits from synthetic-derived wheat and landraces into UK modern wheat germplasm offers scope to raise above-ground biomass and grain yield in moderate-to-low N availability environments

Molecular and cellular mechanisms underlying the evolution of form and function in the amniote jaw.

The amniote jaw complex is a remarkable amalgamation of derivatives from distinct embryonic cell lineages. During development, the cells in these lineages experience concerted movements, migrations, and signaling interactions that take them from their initial origins to their final destinations and imbue their derivatives with aspects of form including their axial orientation, anatomical identity, size, and shape. Perturbations along the way can produce defects and disease, but also generate the variation necessary for jaw evolution and adaptation. We focus on molecular and cellular mechanisms that regulate form in the amniote jaw complex, and that enable structural and functional integration. Special emphasis is placed on the role of cranial neural crest mesenchyme (NCM) during the species-specific patterning of bone, cartilage, tendon, muscle, and other jaw tissues. We also address the effects of biomechanical forces during jaw development and discuss ways in which certain molecular and cellular responses add adaptive and evolutionary plasticity to jaw morphology. Overall, we highlight how variation in molecular and cellular programs can promote the phenomenal diversity and functional morphology achieved during amniote jaw evolution or lead to the range of jaw defects and disease that affect the human condition

Inclusive Search for Anomalous Production of High-pT Like-Sign Lepton Pairs in Proton-Antiproton Collisions at sqrt{s}=1.8 TeV

We report on a search for anomalous production of events with at least two charged, isolated, like-sign leptons with pT > 11 GeV/c using a 107 pb^-1 sample of 1.8 TeV ppbar collisions collected by the CDF detector. We define a signal region containing low background from Standard Model processes. To avoid bias, we fix the final cuts before examining the event yield in the signal region using control regions to test the Monte Carlo predictions. We observe no events in the signal region, consistent with an expectation of 0.63^(+0.84)_(-0.07) events. We present 95% confidence level limits on new physics processes in both a signature-based context as well as within a representative minimal supergravity (tanbeta = 3) model.Comment: 15 pages, 4 figures. Minor textual changes, cosmetic improvements to figures and updated and expanded reference