Can We Study Titin Properties in Passive Myofibrils?

Titin is a giant molecular spring in skeletal and cardiac muscles. It has a variety of important passive, structural, sensing and force-regulatory functions, and thus has been investigated widely (Granzier & Labeit, 2007). Studying the mechanical properties of isolated titin has been difficult because of the enormous size and great instability of this protein. However, the passive properties in single myofibrils are almost exclusively explained by titin, and thus we asked the question if we can study titin properties in intact, passive myofibrils (Bartoo et al., 1997). Single myofibrils were isolated in a standard way (Leonard & Herzog, 2010) and three consecutive stretches of 1.0-3.5μm/sarcomere magnitude were performed at a nominal stretch speed of 0.1 sarcomere length/sarcomere/s. Sarcomere length were measured using a high resolution photo diode array and forces were measured using micro-electronically machined silicon nitrate levers. Single myofibrils frequently showed a distinct change in stiffness upon stretch at sarcomere length of approximately 3.6-3.8μm, they showed a decrease in loading energy with repeat stretch cycles and their efficiency decreased for all loading cycles with increasing stretch magnitude. These properties are in agreement with results observed in single titin preparations (Kellermayer et al., 1997). Therefore, we conclude that titin properties can be studied using single myofibrils. This has at least two significant advantages over tests with isolated titin proteins: (i) testing is technically much easier and (ii) titin is arranged in its intact structural arrangement. In the future, we would like to study titin properties in calcium activated myofibrils in which active (actin-myosin based cross-bridges forces) are eliminated either by chemical inhibition or by deletion of regulatory proteins on actin, as we have done before (Joumaa et al., 2008)

The Mechanical Properties of Titin within a Sarcomere?

Titin is a structural protein in muscle that spans the half sarcomere from z-band to M-line. Although there are selected studies on titin’s mechanical properties from tests on isolated molecules or titin fragments, little is known about its behavior within the structural confines of a sarcomere. Here, we tested the hypothesis that titin properties might be reflected well in single myofibrils. Therefore, the purpose of this study was to measure the passive mechanical properties of isolated single myofibrils and evaluate whether these properties reflect the basic mechanical properties of the titin molecule. Single myofibrils from rabbit psoas were prepared for measurement of passive stretch-shortening cycles at lengths where passive titin forces become important. Three repeat stretch-shortening cycles with magnitudes between 1.0-3.0μm/sarcomere were performed at a speed of 0.1μm/s·sarcomere and repeated after a ten minute rest at zero force. These tests were performed in a relaxation solution (passive) and an activation solution (active) where cross-bridge attachment was inhibited with butanedione monoxime. Myofibrils behaved viscoelastically producing an increased efficiency with repeat stretch-shortening cycles, but a decreased efficiency with increasing stretch magnitudes. Furthermore, we observed a first distinct inflection point in the force-elongation curve at an average sarcomere length of 3.5μm that was associated with an average force of 68±5nN/mm-1. This inflection point was thought to reflect Ig domain unfolding and was missing after a ten minute rest at zero force, suggesting a lack of spontaneous Ig domain refolding. These passive myofibrillar properties are consistent with those observed in isolated titin molecules, suggesting that the mechanics of titin are well preserved in isolated myofibrils, and thus, can be studied readily in myofibrils, rather than in the extremely difficult and labile single titin preparations

Representing Semantified Biological Assays in the Open Research Knowledge Graph

In the biotechnology and biomedical domains, recent text mining efforts advocate for machine-interpretable, and preferably, semantified, documentation formats of laboratory processes. This includes wet-lab protocols, (in)organic materials synthesis reactions, genetic manipulations and procedures for faster computer-mediated analysis and predictions. Herein, we present our work on the representation of semantified bioassays in the Open Research Knowledge Graph (ORKG). In particular, we describe a semantification system work-in-progress to generate, automatically and quickly, the critical semantified bioassay data mass needed to foster a consistent user audience to adopt the ORKG for recording their bioassays and facilitate the organisation of research, according to FAIR principles.Comment: In Proceedings of 'The 22nd International Conference on Asia-Pacific Digital Libraries

Adaptive Low-level Storage of Very Large Knowledge Graphs

The increasing availability and usage of Knowledge Graphs (KGs) on the Web calls for scalable and general-purpose solutions to store this type of data structures. We propose Trident, a novel storage architecture for very large KGs on centralized systems. Trident uses several interlinked data structures to provide fast access to nodes and edges, with the physical storage changing depending on the topology of the graph to reduce the memory footprint. In contrast to single architectures designed for single tasks, our approach offers an interface with few low-level and general-purpose primitives that can be used to implement tasks like SPARQL query answering, reasoning, or graph analytics. Our experiments show that Trident can handle graphs with 10^11 edges using inexpensive hardware, delivering competitive performance on multiple workloads.Comment: Accepted WWW 202

Integrating forest structural diversity measurement into ecological research

The measurement of forest structure has evolved steadily due to advances in technology, methodology, and theory. Such advances have greatly increased our capacity to describe key forest structural elements and resulted in a range of measurement approaches from traditional analog tools such as measurement tapes to highly derived and computationally intensive methods such as advanced remote sensing tools (e.g., lidar, radar). This assortment of measurement approaches results in structural metrics unique to each method, with the caveat that metrics may be biased or constrained by the measurement approach taken. While forest structural diversity (FSD) metrics foster novel research opportunities, understanding how they are measured or derived, limitations of the measurement approach taken, as well as their biological interpretation is crucial for proper application. We review the measurement of forest structure and structural diversity—an umbrella term that includes quantification of the distribution of functional and biotic components of forests. We consider how and where these approaches can be used, the role of technology in measuring structure, how measurement impacts extend beyond research, and current limitations and potential opportunities for future research

Are titin properties reflected in single myofibrils?

Titin is a structural protein in muscle that spans the half sarcomere from Z-band to M-line. Although there are selected studies on titin's mechanical properties from tests on isolated molecules or titin fragments, little is known about its behavior within the structural confines of a sarcomere. Here, we tested the hypothesis that titin properties might be reflected well in single myofibrils. Single myofibrils from rabbit psoas were prepared for measurement of passive stretch-shortening cycles at lengths where passive titin forces occur. Three repeat stretch-shortening cycles with magnitudes between 1.0 and 3.0μm/sarcomere were performed at a speed of 0.1μm/s·sarcomere and repeated after a ten minute rest at zero force. These tests were performed in a relaxation solution (passive) and an activation solution (active) where cross-bridge attachment was inhibited with 2,3 butanedionemonoxime. Myofibrils behaved viscoelastically producing an increased efficiency with repeat stretch-shortening cycles, but a decreased efficiency with increasing stretch magnitudes. Furthermore, we observed a first distinct inflection point in the force-elongation curve at an average sarcomere length of 3.5μm that was associated with an average force of 68±5nN/mm. This inflection point was thought to reflect the onset of Ig domain unfolding and was missing after a ten minute rest at zero force, suggesting a lack of spontaneous Ig domain refolding. These passive myofibrillar properties observed here are consistent with those observed in isolated titin molecules, suggesting that the mechanics of titin are well preserved in isolated myofibrils, and thus, can be studied readily in myofibrils, rather than in the extremely difficult and labile single titin preparations.Canadian Institutes of Health Research - Other ProgramsNatural Sciences and Engineering Research Council - Discovery Gran

HETEROCYCLIC P2Y14 RECEPTOR ANTAGONISTS

Disclosed are compounds of formulas (I)-(IX) for treating or preventing a disease or disorder responsive to antagonism of a P2Y14R receptor agonist in a mammal in need thereof, wherein R1-R8, X, Y, Z, X?, Y?, Z?, and A are as defined herein, that are useful in treating an inflammatory such as asthma, cystic fibrosis, and sterile inflammation of the kidney

Unmanned Aircraft System- (UAS-) Based High-Throughput Phenotyping (HTP) for Tomato Yield Estimation

Yield prediction and variety selection are critical components for assessing production and performance in breeding programs and precision agriculture. Since plants integrate their genetics, surrounding environments, and management conditions, crop phenotypes have been measured over cropping seasons to represent the traits of varieties. These days, UAS (unmanned aircraft system) provides a new opportunity to collect high-quality images and generate reliable phenotypic data efficiently. Here, we propose high-throughput phenotyping (HTP) from multitemporal UAS images for tomato yield estimation. UAS-based RGB and multispectral images were collected weekly and biweekly, respectively. The shape of the features of tomatoes such as canopy cover, canopy, volume, and vegetation indices derived from UAS imagery was estimated throughout the entire season. To extract time-series features from UAS-based phenotypic data, crop growth and growth rate curves were fitted using mathematical curves and first derivative equations. Time-series features such as the maximum growth rate, day at a specific event, and duration were extracted from the fitted curves of different phenotypes. The linear regression model produced high R2 values even with different variable selection methods: all variables (0.79), forward selection (0.7), and backward selection (0.77). With factor analysis, we figured out two significant factors, growth speed and timing, related to high-yield varieties. Then, five time-series phenotypes were selected for yield prediction models explaining 65 percent of the variance in the actual harvest. The phenotypic features derived from RGB images played more important roles in prediction yield. This research also demonstrates that it is possible to select lower-performing tomato varieties successfully. The results from this work may be useful in breeding programs and research farms for selecting high-yielding and disease-/pest-resistant varieties