Novel developments in SBGN-ED and applications

Systems Biology Graphical Notation (SBGN, http://sbgn.org) [1] is an emerging standard for graphical representations of biochemical and cellular processes studied in systems biology. Three different views (Process Description, Entity Relationship, and Activity Flow) cover several aspects of the represented processes in different levels of detail. SBGN helps to communicate biological knowledge more efficient and accurate between different research communities in the life sciences. However, to support SBGN, methods and tools for editing, validating, and translating of SBGN maps are necessary.
We present methods for these tasks and novel developments in SBGN-ED (www.sbgn-ed.org) [2], a tool which allows to create all three types of SBGN maps from scratch, to validate these maps for syntactical and semantical correctness, to translate maps from the KEGG database into SBGN, and to export SBGN maps into several file and image formats. SBGN-ED is based on VANTED (Visualization and Analysis of NeTworks containing Experimental Data, http://www.vanted.org) [3].
As applications of SBGN and SBGN-ED we present furthermore MetaCrop (http://metacrop.ipk-gatersleben.de) [4], a database that summarizes diverse information about metabolic pathways in crop plants, and RIMAS (Regulatory Interaction Maps of Arabidopsis Seed Development, http://rimas.ipk-gatersleben.de) [5], an information portal that provides a comprehensive overview of regulatory pathways and genetic interactions during Arabidopsis embryo and seed development. 

[1] Le Novère, N. et al. (2009) The Systems Biology Graphical Notation. Nature Biotechnology, 27, 735-741.
[2] Czauderna, T., Klukas, C., Schreiber, F. (2010) Editing, validating, and translating of SBGN maps. Bioinformatics, 26 (18), 2340-2341.
[3] Junker, B.H., Klukas, C., Schreiber, F. (2006) VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics, 7, 109+.
[4] Grafahrend-Belau, E., Weise, S., Koschützki, D., Scholz, U., Junker, B.H., Schreiber, F. (2008) MetaCrop - A detailed database of crop plant metabolism. Nucleic Acids Research, 36, D954-D958.
[5] Junker, A., Hartmann, A., Schreiber, F., Bäumlein, H. (2010) An engineer's view on regulation of seed development. Trends in Plant Science, 15(6), 303-307.
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HTPheno: An image analysis pipeline for high-throughput plant phenotyping

<p>Abstract</p> <p>Background</p> <p>In the last few years high-throughput analysis methods have become state-of-the-art in the life sciences. One of the latest developments is automated greenhouse systems for high-throughput plant phenotyping. Such systems allow the non-destructive screening of plants over a period of time by means of image acquisition techniques. During such screening different images of each plant are recorded and must be analysed by applying sophisticated image analysis algorithms.</p> <p>Results</p> <p>This paper presents an image analysis pipeline (HTPheno) for high-throughput plant phenotyping. HTPheno is implemented as a plugin for ImageJ, an open source image processing software. It provides the possibility to analyse colour images of plants which are taken in two different views (top view and side view) during a screening. Within the analysis different phenotypical parameters for each plant such as height, width and projected shoot area of the plants are calculated for the duration of the screening. HTPheno is applied to analyse two barley cultivars.</p> <p>Conclusions</p> <p>HTPheno, an open source image analysis pipeline, supplies a flexible and adaptable ImageJ plugin which can be used for automated image analysis in high-throughput plant phenotyping and therefore to derive new biological insights, such as determination of fitness.</p

Stratiform Host-Rock Replacement via Self-Sustaining Reactions in a Clastic-Dominated (CD-type) Zn Deposit

Stratiform to stratabound replacement of a mixed siliciclastic-carbonate host rock is a defining characteristic of many sediment-hosted base metal deposits. Mineralized rocks in clastic-dominated (CD-type) Zn-Pb ore deposits, which represent our highest value base metal resources, are generally thin (101 m), laterally extensive (103 m), and stratiform to stratabound in fine-grained siltstone and mudstone facies. At the recently discovered Teena CD-type Zn-Pb deposit (Proterozoic Carpentaria province, Australia), the host rock was undergoing burial diagenesis when altered and mineralized by hydrothermal fluids that moved up to 2 km lateral to the fluid input conduit (growth fault) through intraformational intervals. In much of the deposit, carbonate dissolution was an important reaction permeability control, although significant amounts of mineralization also occur in carbonate-free siliciclastic beds. In this study, transmission electron microscopy (TEM) data has been generated on a drill core sample that preserves a sharp reaction front between mineralized and unmineralized domains of the fine-grained siliciclastic compositional end member (carbonate free). Petrographic and mineralogical data provide evidence that oxidized hydrothermal fluids moved through the protolith via reaction permeability that developed from feldspar dissolution. The nature of reactive fluid flow was determined by reactions that took place at the fluid-mineral interface. Pyrite formation during the earliest stage of the hydrothermal paragenesis increased the mineral reactive surface area in the protolith. Acidity was then generated in situ via self-sustaining reactions involving pyrite oxidation, transient Fe sulfate formation, and sphalerite precipitation, which provided positive feedbacks to enhance porosity creation and further fluid infiltration and mineralization. In the absence of carbonate, however, ore fluid pH was buffered by K-feldspar dissolution (~4.5), thereby ensuring sphalerite precipitation was not inhibited under more acidic conditions. All CD-type deposits in the Carpentaria province are hosted by a protolith comprising carbonate, K-feldspar, pyrite, and organic matter; these phases set the boundary conditions for the development of self-sustaining reactions during ore formation. Importantly, these self-sustaining reactions represent a Goldilocks zone for ore formation that is applicable to other sediment-hosted deposits that formed via replacement of mixed siliciclastic-carbonate host rocks (e.g., stratiform Cu)

Nano- and micro-structures in lunar zircon from Apollo 15 and 16 impactites: implications for age interpretations

Meteorite impact processes are ubiquitous on the surfaces of rocky and icy bodies in the Solar System, including the Moon. One of the most common accessory minerals, zircon, when shocked, produces specific micro-structures that may become indicative of the age and shock conditions of these impact processes. To better understand the shock mechanisms in zircon from Apollo 15 and 16 impact breccias, we applied transmission electron microscopy (TEM) and studied nano-structures in eight lunar zircons displaying four different morphologies from breccias 15455, 67915, and 67955. Our observations revealed a range of shock-related features in zircon: (1) planar and non-planar fractures, (2) “columnar” zircon rims around baddeleyite cores, (3) granular textured zircon, in most cases with sub-µm-size inclusions of monoclinic ZrO2 (baddeleyite) and cubic ZrO2 (zirconia), (4) silica-rich glass and metal inclusions of FeS and FeNi present at triple junctions in granular zircon and in baddeleyite, (5) inclusions of rutile in shocked baddeleyite, (6) amorphous domains, (7) recrystallized domains. In many grain aggregates, shock-related micro-structures overprint each other, indicating either different stages of a single impact process or multiple impact events. During shock, some zircons were transformed to diaplectic glass (6), and others (7) were completely decomposed into SiO2 and Zr-oxide, evident from the observed round shapes of cubic zirconia and silica-rich glass filling triple junctions of zircon granules. Despite the highly variable effect on textures and Zr phases, shock-related features show no correlation with relatively homogeneous U–Pb or 207Pb/206Pb ages of zircons. Either the shock events occurred very soon after the solidification or recrystallization of the different Zr phases, or the shock events were too brief to result in noticeable Pb loss during shock metamorphism

Early Life Cognitive Abilities and Body Weight: Cross-Sectional Study of the Association of Inhibitory Control, Cognitive Flexibility, and Sustained Attention with BMI Percentiles in Primary School Children

The objective of this study was to investigate the association of different cognitive abilities with children’s body weight adjusted for further weight influencing sociodemographic, family, and lifestyle factors. Cross-sectional data of 498 primary school children (7.0 ± 0.6 years; 49.8% boys) participating in a health promotion programme in southwest Germany were used. Children performed a computer-based test battery (KiTAP) including an inhibitory control task (Go-Nogo paradigm), a cognitive flexibility task, and a sustained attention task. Height and weight were measured in a standardized manner and converted to BMI percentiles based on national standards. Sociodemographic features (migration background and parental education), family characteristics (parental body weight), and children’s lifestyle (TV consumption, physical activity, consumption of sugar-sweetened beverages and breakfast habits) were assessed via parental questionnaire. A hierarchical regression analysis revealed inhibitory control and cognitive flexibility to be significant cognitive predictors for children’s body weight. There was no association concerning sustained attention. The findings suggest that especially cognitive abilities known as executive functions (inhibitory control and cognitive flexibility) are associated with children’s body weight. Future longitudinal and intervention studies are necessary to investigate the directionality of the association and the potential of integrating cognitive training in obesity prevention strategies. This trial is registered with ClinicalTrials.gov DRKS00000494

FluxMap: A VANTED add-on for the visual exploration of flux distributions in biological networks

<p>Abstract</p> <p>Background</p> <p>The quantification of metabolic fluxes is gaining increasing importance in the analysis of the metabolic behavior of biological systems such as organisms, tissues or cells. Various methodologies (wetlab or drylab) result in sets of fluxes which require an appropriate visualization for interpretation by scientists. The visualization of flux distributions is a necessary prerequisite for intuitive flux data exploration in the context of metabolic networks.</p> <p>Results</p> <p>We present FluxMap, a tool for the advanced visualization and exploration of flux data in the context of metabolic networks. The template-based flux data import assigns flux values and optional quality parameters (e. g. the confidence interval) to biochemical reactions. It supports the discrimination between mass and substance fluxes, such as C- or N-fluxes. After import, flux data mapping and network-based visualization allow the interactive exploration of the dataset. Various visualization options enable the user to adapt layout and network representation according to individual purposes.</p> <p>Conclusions</p> <p>The Vanted add-on FluxMap comprises a comprehensive set of functionalities for visualization and advanced visual exploration of flux distributions in biological networks. It is available as a Java open source tool from http://www.vanted.org/fluxmap.</p

A human phospholipid phosphatase activated by a transmembrane control module

In voltage-sensitive phosphatases (VSPs), a transmembrane voltage sensor domain (VSD) controls an intracellular phosphoinositide phosphatase domain, thereby enabling immediate initiation of intracellular signals by membrane depolarization. The existence of such a mechanism in mammals has remained elusive, despite the presence of VSP-homologous proteins in mammalian cells, in particular in sperm precursor cells. Here we demonstrate activation of a human VSP (hVSP1/TPIP) by an intramolecular switch. By engineering a chimeric hVSP1 with enhanced plasma membrane targeting containing the VSD of a prototypic invertebrate VSP, we show that hVSP1 is a phosphoinositide-5-phosphatase whose predominant substrate is PI(4,5)P(2). In the chimera, enzymatic activity is controlled by membrane potential via hVSP1\u27s endogenous phosphoinositide binding motif. These findings suggest that the endogenous VSD of hVSP1 is a control module that initiates signaling through the phosphatase domain and indicate a role for VSP-mediated phosphoinositide signaling in mammals

Study protocol for a randomised controlled trial to determine the effectiveness of a mHealth application as a family supportive tool in paediatric otolaryngology perioperative process (TONAPP)

Background: Otorhinolaryngology (ORL) surgery is common in children, but hospitalisation, surgery, and home care after discharge are stressful experiences for young patients and their family caregivers. Findings from literature highlight a lack of time in hospitals to support ORL surgery children and their caregivers through the perioperative process, along with the risks of caregivers' autonomous web or social media resources investigation. Therefore, this study aims to evaluate the effectiveness of a mobile health application with content to support ORL patients and their caregivers in the perioperative period to reduce caregiver anxiety and child distress compared to standard care. Methods: An open-label, two-arm randomised control trial design is being adopted. The intervention consists of a mobile health application with content to support ORL patients and their caregivers during the perioperative period. One hundred eighty participants will be enrolled and randomly assigned to the experimental group using the mHealth application or the control group. The control group receives standard information and education about the ORL perioperative period from healthcare providers orally or through brochures. The primary outcome is the difference between the intervention and control groups in preoperative caregiver state anxiety. Secondary outcome measures include children's distress before surgery and family preparation for hospitalisation. Discussion: The results of this study will be critical to the implementation of a new and safe model for the management of care and education in paediatrics. This model can achieve positive organisational and health outcomes by supporting continuity of care and empowering citizens to have informed participation and satisfaction in paediatric health promotion and management. Trial registration: Trial identifier: NCT05460689 registry name: ClinicalTrials.gov. Date of registration: July 15, 2022. Last update posted: February 23, 2023