Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016

Standards are essential to the advancement of science and technology. In systems and synthetic biology, numerous standards and associated tools have been developed over the last 16 years. This special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards, as well as to provide centralised and easily citable access to them

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016

Standards are essential to the advancement of science and technology. In systems and synthetic biology, numerous standards and associated tools have been developed over the last 16 years. This special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards, as well as to provide centralised and easily citable access to them

Observing a column-dependent zeta in dense interstellar sources: the case of the Horsehead Nebula

Context: Observations of small carbon-bearing molecules such as CCH, C4H, c-C3H2, and HCO in the Horsehead Nebula have shown these species to have higher abundances towards the edge of the source than towards the center. Aims: Given the determination of a wide range of values for zeta (s-1), the total ionization rate of hydrogen atoms, and the proposal of a column-dependent zeta(N_H), where N_H is the total column of hydrogen nuclei, we desire to determine if the effects of zeta(N_H) in a single object with spatial variation can be observable. We chose the Horsehead Nebula because of its geometry and high density. Method: We model the Horsehead Nebula as a near edge-on photon dominated region (PDR), using several choices for zeta, both constant and as a function of column. The column-dependent zeta functions are determined by a Monte Carlo model of cosmic ray penetration, using a steep power-law spectrum and accounting for ionization and magnetic field effects. We consider a case with low-metal elemental abundances as well as a sulfur-rich case. Results: We show that use of a column-dependent zeta(N_H) of 5(-15) s-1 at the surface and 7.5(-16) s-1 at Av = 10 on balance improves agreement between measured and theoretical molecular abundances, compared with constant values of zeta.Comment: 12 pages, 6 figures, 5 tables, accepted in A&

Walk well:a randomised controlled trial of a walking intervention for adults with intellectual disabilities: study protocol

Background - Walking interventions have been shown to have a positive impact on physical activity (PA) levels, health and wellbeing for adult and older adult populations. There has been very little work carried out to explore the effectiveness of walking interventions for adults with intellectual disabilities. This paper will provide details of the Walk Well intervention, designed for adults with intellectual disabilities, and a randomised controlled trial (RCT) to test its effectiveness. Methods/design - This study will adopt a RCT design, with participants allocated to the walking intervention group or a waiting list control group. The intervention consists of three PA consultations (baseline, six weeks and 12 weeks) and an individualised 12 week walking programme. A range of measures will be completed by participants at baseline, post intervention (three months from baseline) and at follow up (three months post intervention and six months from baseline). All outcome measures will be collected by a researcher who will be blinded to the study groups. The primary outcome will be steps walked per day, measured using accelerometers. Secondary outcome measures will include time spent in PA per day (across various intensity levels), time spent in sedentary behaviour per day, quality of life, self-efficacy and anthropometric measures to monitor weight change. Discussion - Since there are currently no published RCTs of walking interventions for adults with intellectual disabilities, this RCT will examine if a walking intervention can successfully increase PA, health and wellbeing of adults with intellectual disabilities

Partitioning a regional groundwater flow system into shallow local and deep regional flow compartments

International audienceThe distribution of groundwater fluxes in aquifers is strongly influenced by topography, and organized between hillslope and regional scales. The objective of this study is to provide new insights regarding the compartmentalization of aquifers at the regional scale and the partitioning of recharge between shallow/local and deep/regional groundwater transfers. A finite-difference flow model was implemented, and the flow structure was analyzed as a function of recharge (from 20 to 500 mm/yr), at the regional-scale (1400 km2), in three dimensions, and accounting for variable groundwater discharge zones; aspects which are usually not considered simultaneously in previous studies. The model allows visualizing 3-D circulations, as those provided by Tothian models in 2-D, and shows local and regional transfers, with 3-D effects. The probability density function of transit times clearly shows two different parts, interpreted using a two-compartment model, and related to regional groundwater transfers and local groundwater transfers. The role of recharge on the size and nature of the flow regimes, including groundwater pathways, transit time distributions, and volumes associated to the two compartments, have been investigated. Results show that topography control on the water table and groundwater compartmentalization varies with the recharge rate applied. When recharge decreases, the absolute value of flow associated to the regional compartment decreases, whereas its relative value increases. The volume associated to the regional compartment is calculated from the exponential part of the two-compartment model, and is nearly insensitive to the total recharge fluctuations

Harmonizing semantic annotations for computational models in biology

Life science researchers use computational models to articulate and test hypotheses about the behavior of biological systems. Semantic annotation is a critical component for enhancing the interoperability and reusability of such models as well as for the integration of the data needed for model parameterization and validation. Encoded as machine-readable links to knowledge resource terms, semantic annotations describe the computational or biological meaning of what models and data represent. These annotations help researchers find and repurpose models, accelerate model composition and enable knowledge integration across model repositories and experimental data stores. However, realizing the potential benefits of semantic annotation requires the development of model annotation standards that adhere to a community-based annotation protocol.Without such standards, tool developers must account for a variety of annotation formats and approaches, a situation that can become prohibitively cumbersome and which can defeat the purpose of linking model elements to controlled knowledge resource terms. Currently, no consensus protocol for semantic annotation exists among the larger biological modeling community. Here, we report on the landscape of current annotation practices among the Computational Modeling in BIology NEtwork community and provide a set of recommendations for building a consensus approach to semantic annotation

Mutations in GPAA1, Encoding a GPI Transamidase Complex Protein, Cause Developmental Delay, Epilepsy, Cerebellar Atrophy, and Osteopenia.

Approximately one in every 200 mammalian proteins is anchored to the cell membrane through a glycosylphosphatidylinositol (GPI) anchor. These proteins play important roles notably in neurological development and function. To date, more than 20 genes have been implicated in the biogenesis of GPI-anchored proteins. GPAA1 (glycosylphosphatidylinositol anchor attachment 1) is an essential component of the transamidase complex along with PIGK, PIGS, PIGT, and PIGU (phosphatidylinositol-glycan biosynthesis classes K, S, T, and U, respectively). This complex orchestrates the attachment of the GPI anchor to the C terminus of precursor proteins in the endoplasmic reticulum. Here, we report bi-allelic mutations in GPAA1 in ten individuals from five families. Using whole-exome sequencing, we identified two frameshift mutations (c.981_993del [p.Gln327Hisfs∗102] and c.920delG [p.Gly307Alafs∗11]), one intronic splicing mutation (c.1164+5C>T), and six missense mutations (c.152C>T [p.Ser51Leu], c.160_161delinsAA [p.Ala54Asn], c.527G>C [p.Trp176Ser], c.869T>C [p.Leu290Pro], c.872T>C [p.Leu291Pro], and c.1165G>C [p.Ala389Pro]). Most individuals presented with global developmental delay, hypotonia, early-onset seizures, cerebellar atrophy, and osteopenia. The splicing mutation was found to decrease GPAA1 mRNA. Moreover, flow-cytometry analysis of five available individual samples showed that several GPI-anchored proteins had decreased cell-surface abundance in leukocytes (FLAER, CD16, and CD59) or fibroblasts (CD73 and CD109). Transduction of fibroblasts with a lentivirus encoding the wild-type protein partially rescued the deficiency of GPI-anchored proteins. These findings highlight the role of the transamidase complex in the development and function of the cerebellum and the skeletal system

Observation by an Air-Shower Array in Tibet of the Multi-TeV Cosmic-Ray Anisotropy due to Terrestrial Orbital Motion Around the Sun

We report on the solar diurnal variation of the galactic cosmic-ray intensity observed by the Tibet III air shower array during the period from 1999 to 2003. In the higher-energy event samples (12 TeV and 6.2 TeV), the variations are fairly consistent with the Compton-Getting anisotropy due to the terrestrial orbital motion around the sun, while the variation in the lower-energy event sample (4.0 TeV) is inconsistent with this anisotropy. This suggests an additional anisotropy superposed at the multi-TeV energies, e.g. the solar modulation effect. This is the highest-precision measurement of the Compton-Getting anisotropy ever made.Comment: 4 pages, 2 figures, includes .bbl fil