Principles for Understanding the Accuracy of SHAPE-Directed RNA Structure Modeling

Accurate RNA structure modeling is an important, incompletely solved, challenge. Single-nucleotide resolution SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) yields an experimental measurement of local nucleotide flexibility that can be incorporated as pseudo-free energy change constraints to direct secondary structure predictions. Prior work from our laboratory has emphasized both the overall accuracy of this approach and the need for nuanced interpretation of some apparent discrepancies between modeled and accepted structures. Recent studies by Das and colleagues [Kladwang et al., Biochemistry 50:8049 (2011) and Nat. Chem. 3:954 (2011)], focused on analyzing six small RNAs, yielded poorer RNA secondary structure predictions than expected based on prior benchmarking efforts. To understand the features that led to these divergent results, we re-examined four RNAs yielding the poorest results in this recent work – tRNAPhe, the adenine and cyclic-di-GMP riboswitches, and 5S rRNA. Most of the errors reported by Das and colleagues reflected non-standard experiment and data processing choices, and selective scoring rules. For two RNAs, tRNAPhe and the adenine riboswitch, secondary structure predictions are nearly perfect if no experimental information is included but were rendered inaccurate by the Das and colleagues SHAPE data. When best practices were used, single-sequence SHAPE-directed secondary structure modeling recovered ~93% of individual base pairs and greater than 90% of helices in the four RNAs, essentially indistinguishable from the mutate-and-map approach with the exception of a single helix in the 5S rRNA. The field of experimentally-directed RNA secondary structure prediction is entering a phase focused on the most difficult prediction challenges. We outline five constructive principles for guiding this field forward

Extending the spectrum of Ellis van Creveld syndrome: a large family with a mild mutation in the EVC gene

<p>Abstract</p> <p>Background</p> <p>Ellis-van Creveld (EvC) syndrome is characterized by short limbs, short ribs, postaxial polydactyly, dysplastic nails and teeth and is inherited in an autosomal recessive pattern. We report a family with complex septal cardiac defects, rhizomelic limb shortening, and polydactyly, without the typical lip, dental, and nail abnormalities of EvC. The phenotype was inherited in an autosomal recessive pattern, with one instance of pseudodominant inheritance.</p> <p>Methods</p> <p>Because of the phenotypic overlap with EvC, microsatellite markers were used to test for linkage to the <it>EVC/EVC2 </it>locus. The results did not exclude linkage, so samples were sequenced for mutations.</p> <p>Results</p> <p>We identified a c.1868T>C mutation in <it>EVC</it>, which predicts p.L623P, and was homozygous in affected individuals.</p> <p>Conclusion</p> <p>We conclude that this <it>EVC </it>mutation is hypomorphic and that such mutations can cause a phenotype of cardiac and limb defects that is less severe than typical EvC. <it>EVC </it>mutation analysis should be considered in patients with cardiac and limb malformations, even if they do not manifest typical EvC syndrome.</p

Extending the spectrum of Ellis van Creveld syndrome: a large family with a mild mutation in the EVC gene

<p>Abstract</p> <p>Background</p> <p>Ellis-van Creveld (EvC) syndrome is characterized by short limbs, short ribs, postaxial polydactyly, dysplastic nails and teeth and is inherited in an autosomal recessive pattern. We report a family with complex septal cardiac defects, rhizomelic limb shortening, and polydactyly, without the typical lip, dental, and nail abnormalities of EvC. The phenotype was inherited in an autosomal recessive pattern, with one instance of pseudodominant inheritance.</p> <p>Methods</p> <p>Because of the phenotypic overlap with EvC, microsatellite markers were used to test for linkage to the <it>EVC/EVC2 </it>locus. The results did not exclude linkage, so samples were sequenced for mutations.</p> <p>Results</p> <p>We identified a c.1868T>C mutation in <it>EVC</it>, which predicts p.L623P, and was homozygous in affected individuals.</p> <p>Conclusion</p> <p>We conclude that this <it>EVC </it>mutation is hypomorphic and that such mutations can cause a phenotype of cardiac and limb defects that is less severe than typical EvC. <it>EVC </it>mutation analysis should be considered in patients with cardiac and limb malformations, even if they do not manifest typical EvC syndrome.</p

An efficient memory allocation algorithm and hardware design with VHDL synthesis

This paper presents a hardware-efficient memory allocation technique, called EMA, that detects the existence of any free block of requested size in memory. EMA can allocate a free memory block of any number of chunks in any part of memory without having any internal fragmentation. The gate-level design of the hardware unit, along with its area-time measurements is given in this paper. Simulation results indicate that EMA is fast and flexible enough to allocate/deallocate a free block in any part of memory resulting in efficient utilization of memory spaces. In addition, the VHDL synthesis with FPGA implementation shows that EMA has less complicated hardware, and is faster than the known hardware techniques

Autonomic nervous system functions in obese children

Childhood obesity is a complex syndrome, probably due to the multiplicity of contributing factors, contradictory literature information about etiology, prognosis, prevention and treatment. In the recent reports, autonomic nervous system (ANS) dysfunction has been documented in adult obesity. Autonomic nervous system functions in obese children are not clear. This study was planned to investigate autonomic nervous system function in childhood (7-13 years of age) obesity. Study and control groups consisted of 33 simple obese (23 boys and ten girls, mean age 9.5 +/- 1.4 years) and 30 healthy children (18 boys and 12 girls, mean age 10.1 +/- 1.8 years), respectively. Four non-invasive autonomic nervous system function tests (Orthostatic test, Valsalva ratio, 30/15 ratio, Heart rate responses to deep breathing) and general ophthalmic examination were performed on both groups. The difference between the obese and control groups was found statistically significant in Valsalva ratio, 30/15 ratio and Heart rate responses to deep breathing (P 0.05). Ophthalmic examinations were normal. The result of these tests suggested normal activity of sympathetic, and hypoactivity of parasympathetic nervous system, implying parasympathetic nervous system dysfunction as a risk factor or associated finding in childhood obesity. (C) 2000 Elsevier Science B.V. All rights reserved

Enuresis prevalence and accompanying factors in schoolchildren: A questionnaire study from Southeast Anatolia

Introduction: The aims of this study were to establish the prevalence of enuresis, to determine accompanying factors, and to identify common methods in the management of enuresis in Turkish children aged between 6 and 11 years living in eastern Anatolia. Methods: The parents of 3,527 schoolchildren aged between 6 and 11 years completed a self-administered questionnaire. The questionnaire asked about sociodemographic data, enuresis data, physical or psychological disorders, and family stressors. Descriptive statistics and chi(2) test were used for data analysis. Results: The response rate was 88%. The overall prevalence of reported enuresis was 12.96%, and the prevalence of marked enuresis ( at least weekly) was 9.8%. Enuresis was notably more common in boys ( male: female ratio 1.6), and the prevalence rates decreased by age without gender bias. Of all enuretic children, 21% had also daytime bed-wetting. The rate of a positive family history was 42% for siblings only and 66% for the other family members. Significantly more of the dry children woke up spontaneously at night to void as compared with the enuretic children ( p < 0.001). The parental concern level was not high, and only 15% of the children visited a physician for the management of enuresis. Low socioeconomic status, unfavorable perinatal or postnatal history, and unsatisfactory familial characteristics were significantly more frequent in the enuretic group (p < 0.05). The enuretic children had also higher rates of poor school performance and poor social adaptation as compared with nonenuretic children (p < 0.001). Conclusions: These results suggest that the prevalence of enuresis in eastern Anatolia is similar to that reported from western Anatolia and from most other countries. Turkish families did not report a high-level concern about enuresis, and the problem was managed primarily within the family. Copyright (C) 2004 S. Karger AG, Basel