Mapping Physical Formats to Logical Models to Extract Data and Metadata: The Defuddle Parsing Engine

Scientists, fueled by the desire for systems-level understanding of phenomena, increasingly need to share their results across multiple disciplines. Accomplishing this requires data to be annotated, contextualized, and readily searchable and translated into other formats. While these requirements can be addressed by custom programming or obviated by community standardization, neither approach has ‘solved’ the problem. In this paper, we describe a complementary approach – a general capability for articulating the format of arbitrary textual and binary data using a logical data model, expressed in XML-Schema, which can be used to provide annotation and context, extract metadata, and enable translation. This work is based on the draft specification for the Data Format Description Language and our open source “Defuddle” parser. We present an overview of the specification, detail the design of Defuddle, and discuss the benefits and challenges of this general approach to enabling discovery and sharing of diverse data sets

Reductions in mesophyll and guard cell photosynthesis impact on the control of stomatal responses to light and CO2

Transgenic antisense tobacco plants with a range of reductions in sedoheptulose-1,7-bisphosphatase (SBPase) activity were used to investigate the role of photosynthesis in stomatal opening responses. High resolution chlorophyll a fluorescence imaging showed that the quantum efficiency of photosystem II electron transport (Fq′/Fm′) was decreased similarly in both guard and mesophyll cells of the SBPase antisense plants compared to the wild-type plants. This demonstrated for the first time that photosynthetic operating efficiency in the guard cells responds to changes in the regeneration capacity of the Calvin cycle. The rate of stomatal opening in response to a 30 min, 10-fold step increase in red photon flux density in the leaves from the SBPase antisense plants was significantly greater than wild-type plants. Final stomatal conductance under red and mixed blue/red irradiance was greater in the antisense plants than in the wild-type control plants despite lower CO2 assimilation rates and higher internal CO2 concentrations. Increasing CO2 concentration resulted in a similar stomatal closing response in wild-type and antisense plants when measured in red light. However, in the antisense plants with small reductions in SBPase activity greater stomatal conductances were observed at all Ci levels. Together, these data suggest that the primary light-induced opening or CO2-dependent closing response of stomata is not dependent upon guard or mesophyll cell photosynthetic capacity, but that photosynthetic electron transport, or its end-products, regulate the control of stomatal responses to light and CO2. © 2008 The Author(s)

MFA11 (MFA 2011)

Catalogue of a culminating student exhibition held at the Mildred Lane Kemper Art Museum, May 6-Aug. 1, 2011. Content includes Introduction / Buzz Spector -- Patricia Olynyk -- Marshall N. Klimasewiski -- John Talbott Allen -- Meghan Bean -- Shira Berkowitz / Maggie Stanley Majors -- Darrick Byers, Bryce Olen Robinson -- Jisun Choi -- Zlatko Ćosić -- James R. Daniels -- Kara Daving -- Andrea Degener -- Kristin Fleischmann / Randi Shapiro -- William Frank / Lawrence Ypil -- Nicholas Kania -- Katherine McCullough -- Jordan McGirk / Aditi Machado -- Zachary Miller -- Esther Murphy / Maggie Stanley Majors -- Kathryn Neale -- Christopher Ottinger / Melissa Olson -- Maia Palmer -- Nicole Petrescu / Melissa Olson -- Lauren Pressler / Randi Shapiro -- Whitney Sage / Aliya A. Reich -- Donna Smith.https://openscholarship.wustl.edu/books/1005/thumbnail.jp

SHAPE analysis of the FIV Leader RNA reveals a structural switch potentially controlling viral packaging and genome dimerization

Feline immunodeficiency virus (FIV) infects many species of cat, and is related to HIV, causing a similar pathology. High-throughput selective 2′ hydroxyl acylation analysed by primer extension (SHAPE), a technique that allows structural interrogation at each nucleotide, was used to map the secondary structure of the FIV packaging signal RNA. Previous studies of this RNA showed four conserved stem–loops, extensive long-range interactions (LRIs) and a small, palindromic stem–loop (SL5) within the gag open reading frame (ORF) that may act as a dimerization initiation site (DIS), enabling the virus to package two copies of its genome. Our analyses of wild-type (wt) and mutant RNAs suggest that although the four conserved stem–loops are static structures, the 5′ and 3′ regions previously shown to form LRI also adopt an alternative, yet similarly conserved conformation, in which the putative DIS is occluded, and which may thus favour translational and splicing functions over encapsidation. SHAPE and in vitro dimerization assays were used to examine SL5 mutants. Dimerization contacts appear to be made between palindromic loop sequences in SL5. As this stem–loop is located within the gag ORF, recognition of a dimeric RNA provides a possible mechanism for the specific packaging of genomic over spliced viral RNAs

RNA secondary structure of the feline immunodeficiency virus 5′UTR and Gag coding region

The 5′ untranslated region (5′UTR) of lentiviral genomic RNA is highly structured, and is the site of multiple RNA–RNA and RNA–protein interactions throughout the viral life cycle. The 5′UTR plays a critical role during transcription, translational regulation, genome dimerization, reverse transcription priming and encapsidation. The 5′UTR structures of human lentiviruses have been extensively studied, yet the respective role and conformation of each domain is still controversial. To gain insight into the structure-function relationship of lentiviral 5′UTRs, we modelled the RNA structure of the feline immunodeficiency virus (FIV), a virus that is evolutionarily distant from the primate viruses. Through combined chemical and enzymatic structure probing and a thorough phylogenetic study, we establish a model for the secondary structure of the 5′UTR and Gag coding region. This work highlights properties common to all lentiviruses, like the primer binding site structure and the presence of a stable stem-loop at the 5′ extremity. We find that FIV has also evolved specific features, including a long stem loop overlapping the end of the 5′UTR and the beginning of the coding region. In addition, we observed footprints of Gag protein on each side of the initiation codon, this sheds light on the role of the sequences required for encapsidation

Locomotor recovery following contusive spinal cord injury does not require oligodendrocyte remyelination

The contribution of oligodendrocytes to remyelination in functional recovery after spinal cord injury is not fully understood. Here, the authors show that oligodendrocyte progenitor cell differentiation is not required for functional recovery after spinal cord injury in mice

Highlights From the Annual Meeting of the American Epilepsy Society 2022

With more than 6000 attendees between in-person and virtual offerings, the American Epilepsy Society Meeting 2022 in Nashville, felt as busy as in prepandemic times. An ever-growing number of physicians, scientists, and allied health professionals gathered to learn a variety of topics about epilepsy. The program was carefully tailored to meet the needs of professionals with different interests and career stages. This article summarizes the different symposia presented at the meeting. Basic science lectures addressed the primary elements of seizure generation and pathophysiology of epilepsy in different disease states. Scientists congregated to learn about anti-seizure medications, mechanisms of action, and new tools to treat epilepsy including surgery and neurostimulation. Some symposia were also dedicated to discuss epilepsy comorbidities and practical issues regarding epilepsy care. An increasing number of patient advocates discussing their stories were intertwined within scientific activities. Many smaller group sessions targeted more specific topics to encourage member participation, including Special Interest Groups, Investigator, and Skills Workshops. Special lectures included the renown Hoyer and Lombroso, an ILAE/IBE joint session, a spotlight on the impact of Dobbs v. Jackson on reproductive health in epilepsy, and a joint session with the NAEC on coding and reimbursement policies. The hot topics symposium was focused on traumatic brain injury and post-traumatic epilepsy. A balanced collaboration with the industry allowed presentations of the latest pharmaceutical and engineering advances in satellite symposia