Rfam: Wikipedia, clans and the “decimal” release

The Rfam database aims to catalogue non-coding RNAs through the use of sequence alignments and statistical profile models known as covariance models. In this contribution, we discuss the pros and cons of using the online encyclopedia, Wikipedia, as a source of community‐derived annotation. We discuss the addition of groupings of related RNA families into clans and new developments to the website. Rfam is available on the Web at http://rfam.sanger.ac.uk

Maternal and offspring intelligence in relation to BMI across childhood and adolescence

Objective: The present study tested the association between both mothers’ and offspring’s intelligence and offspring’s body mass index (BMI) in youth. Method: Participants were members of the National Longitudinal Survey of Youth 1979 (NLSY-79) Children and Young Adults cohort (n = 11,512) and their biological mothers who were members of the NLSY-79 (n = 4932). Offspring’s IQ was measured with the Peabody Individual Achievement Test (PIAT). Mothers’ IQ was measured with the Armed Forces Qualification Test (AFQT). A series of regression analyses tested the association between IQ and offspring’s BMI by age group, while adjusting for pre-pregnancy BMI and family SES. The analyses were stratified by sex and ethnicity (non-Black and non-Hispanic, Black, and Hispanic). Results: The following associations were observed in the fully adjusted analyses. For the non-Blacks and non-Hispanics, a SD increment in mothers’ IQ was negatively associated with daughters’ BMI across all age-groups, ranging from β = −0.12 (95% CI −0.22 to −0.02, p = 0.021) in late childhood, to β = −0.17 (95% C.I. −0.27 to −0.07, p = 0001), in early adolescence and a SD increment in boys’ IQ was positively associated with their BMI in early adolescence β = 0.09 (95% CI 0.01–0.18, p = 0.031). For Blacks, there was a non-linear relationship between mothers’ IQ and daughters’ BMI across childhood and between girls’ IQ and BMI across adolescence. There was a positive association between mothers’ IQ and sons’ BMI in early adolescence (β = 0.17, 95% CI 0.02–0.32, p = 0.030). For Hispanic boys, there was a positive IQ-BMI association in late childhood (β = 0.19, 95% CI 0.05–0.33, p = 0.008) and early adolescence (β = 0.17, 95% CI 0.04–0.31, p = 0.014). Conclusion: Mothers’ IQ and offspring’s IQ were associated with offspring’s BMI. The relationships varied in direction and strength across ethnicity, age group and sex. Obesity interventions may benefit from acknowledging the heterogeneous influence that intelligence has on childhood BMI

Nonviral Approaches for Neuronal Delivery of Nucleic Acids

The delivery of therapeutic nucleic acids to neurons has the potential to treat neurological disease and spinal cord injury. While select viral vectors have shown promise as gene carriers to neurons, their potential as therapeutic agents is limited by their toxicity and immunogenicity, their broad tropism, and the cost of large-scale formulation. Nonviral vectors are an attractive alternative in that they offer improved safety profiles compared to viruses, are less expensive to produce, and can be targeted to specific neuronal subpopulations. However, most nonviral vectors suffer from significantly lower transfection efficiencies than neurotropic viruses, severely limiting their utility in neuron-targeted delivery applications. To realize the potential of nonviral delivery technology in neurons, vectors must be designed to overcome a series of extra- and intracellular barriers. In this article, we describe the challenges preventing successful nonviral delivery of nucleic acids to neurons and review strategies aimed at overcoming these challenges

GAMETOPHYTE DEFECTIVE 1, a Putative Subunit of RNases P/MRP, Is Essential for Female Gametogenesis and Male Competence in Arabidopsis

RNA biogenesis, including biosynthesis and maturation of rRNA, tRNA and mRNA, is a fundamental process that is critical for cell growth, division and differentiation. Previous studies showed that mutations in components involved in RNA biogenesis resulted in abnormalities in gametophyte and leaf development in Arabidopsis. In eukaryotes, RNases P/MRP (RNase mitochondrial RNA processing) are important ribonucleases that are responsible for processing of tRNA, and transcription of small non-coding RNAs. Here we report that Gametophyte Defective 1 (GAF1), a gene encoding a predicted protein subunit of RNases P/MRP, AtRPP30, plays a role in female gametophyte development and male competence. Embryo sacs were arrested at stages ranging from FG1 to FG7 in gaf1 mutant, suggesting that the progression of the gametophytic division during female gametogenesis was impaired in gaf1 mutant. In contrast, pollen development was not affected in gaf1. However, the fitness of the mutant pollen tube was weaker than that of the wild-type, leading to reduced transmission through the male gametes. GAF1 is featured as a typical RPP30 domain protein and interacts physically with AtPOP5, a homologue of RNases P/MRP subunit POP5 of yeast. Together, our data suggest that components of the RNases P/MRP family, such as RPP30, play important roles in gametophyte development and function in plants

Shear Wave Velocity Profiling with Surface Wave Methods

Surface wave method was introduced as a tool to the geotechnical and infrastructure engineering fields in the early 1980\u27s. Since then, the method has been continuously modified and improved. The adoption of the method has accelerated in the last ten years because of the interest of the engineering community, and due to the development of affordable and portable hardware and software. Despite numerous studies that demonstrate its effectiveness in a wide spectrum of applications, the method has not been fully embraced by the engineering community mainly due to lack of standardization. The common attributes of different approaches in implementing the surface method from the point of view of the engineering applications are discussed, followed by the practical and theoretical strengths and limitations of alternative approaches. Different approaches should provide satisfactory results as long as the inherent limitations of each approach are matched with the requirements of the engineering objectives of a given project

Implementation of LRFD Methods to Quantify Value of Site Characterization

A comprehensive research program was recently completed to develop state specific LRFD guidelines for the Missouri Department of Transportation in the United States of America (USA). The new guidelines implement improvements to current AASHTO LRFD specifications that provide minimum national standards for design of transportation projects in the USA. The most notable of these improvements are specification of resistance factors that are dependent upon the variability of input parameters. One product of these improvements is to produce designs that more closely achieve target levels of reliability. Perhaps more importantly, the guidelines provide designers with explicit means to quantify the potential value of site characterization activities during the design phase. The latter outcome allows designers to make more rational decisions regarding the type and scope of site characterization activities and provides quantitative support for such decisions so that designers can more effectively convey the value of site characterization to others

MoDOT Research Program to Improve Design of Bridge Foundations

Like other state departments of transportation, the Missouri Department of Transportation (MoDOT) has recently transitioned to load and resistance factor design (LRFD) methods for design of bridge foundations and other geotechnical structures within the state. With this transition, the opportunity exists to evaluate and improve upon traditional design procedures and methods to produce substantial cost savings for the agency and taxpayers of the state while maintaining appropriate and consistent performance and risk. With this objective in mind, MoDOT has recently embarked on a comprehensive research program intended to holistically look for ways to improve design procedures (interpreted broadly) for the benefit of the agency and public. The geotechnical aspects of this research are being collaboratively performed by the authors along with their students from the University of Missouri and Missouri University of Science and Technology. The specific geotechnical applications selected for the research program include design of bridge foundations including drilled shafts, driven piles, and spread footings, and design of earth slopes and embankments. The deliverables to be produced through the work include a revised design specification for bridge foundations, a new design specification for earth slopes and embankments, and several design commentary documents that will provide justification and explanations for the provisions in the design specifications themselves. Principal funding for the research is being provided by MoDOT with additional funding being provided by the National University Transportation Center at Missouri S&T and the University of Missouri. The two year research program began in November 2008 and will be completed in October 2010. This article provides a summary of the motivation and objectives for this ongoing research program along with a summary of the major activities being undertaken with a focus on the aspects of this work related to using drilled shafts for bridge foundations