Feeding postural behaviors and food geometric and material properties in bearded capuchin monkeys (Sapajus libidinosus)

Foods that are geometrically and mechanically challenging to eat have been associated with specializations in feeding behavior and craniodental morphology across primates, and many of these foods are embedded, requiring a variety of positional behaviors during feeding. However, variation in positional behaviors in response to food properties is not well understood. Here, we examine differences in feeding postural behaviors across feeding events in relation to substrate and food geometric and material properties in a species of extractive foragers, bearded capuchins (Sapajus libidinosus).Methods and materialsWe coded over 1400 co-occurring postural and feeding behaviors, their durations, and relative sizes of substrate and food from videos recorded at Fazenda Boa Vista in Gilbués, Piauí, Brazil. Food material properties were measured from foods collected at the time of the video recordings.ResultsOur results suggest that bearded capuchin feeding postures significantly differ across the feeding sequence, with substrate size, and between foods of high and low toughness and elastic modulus. Feeding postures were less variable for highly mechanically challenging foods. Food size also had a significant effect on postural behaviors. Large foods were more likely to be associated with suspended postures and small foods with sitting and squatting. Feeding postural behaviors were best explained by a combination of substrate and food variables.ConclusionsOur results indicate that food geometric and mechanical properties have a significant influence on feeding postural behaviors in bearded capuchins. We posit that feeding postural behaviors reflect a combination of substrate variables and food properties, and large, mechanically challenging foods have a limiting effect on postural variation.<br

Why reinvent the wheel: Let's build question answering systems together

Modern question answering (QA) systems need to flexibly integrate a number of components specialised to fulfil specific tasks in a QA pipeline. Key QA tasks include Named Entity Recognition and Disambiguation, Relation Extraction, and Query Building. Since a number of different software components exist that implement different strategies for each of these tasks, it is a major challenge to select and combine the most suitable components into a QA system, given the characteristics of a question. We study this optimisation problem and train classifiers, which take features of a question as input and have the goal of optimising the selection of QA components based on those features. We then devise a greedy algorithm to identify the pipelines that include the suitable components and can effectively answer the given question. We implement this model within Frankenstein, a QA framework able to select QA components and compose QA pipelines. We evaluate the effectiveness of the pipelines generated by Frankenstein using the QALD and LC-QuAD benchmarks. These results not only suggest that Frankenstein precisely solves the QA optimisation problem but also enables the automatic composition of optimised QA pipelines, which outperform the static Baseline QA pipeline. Thanks to this flexible and fully automated pipeline generation process, new QA components can be easily included in Frankenstein, thus improving the performance of the generated pipelines

Atomic Resolution Cryo-EM Structure Of A Nativelike CENP-A Nucleosome Aided By An Antibody Fragment

Genomic DNA in eukaryotes is organized into chromatin through association with core histones to form nucleosomes, each distinguished by their DNA sequences and histone variants. Here, we used a single-chain antibody fragment (scFv) derived from the anti-nucleosome antibody mAb PL2-6 to stabilize human CENP-A nucleosome containing a native α-satellite DNA and solved its structure by the cryo-electron microscopy (cryo-EM) to 2.6 Å resolution. In comparison, the corresponding cryo-EM structure of the free CENP-A nucleosome could only reach 3.4 Å resolution. We find that scFv binds to a conserved acidic patch on the histone H2A-H2B dimer without perturbing the nucleosome structure. Our results provide an atomic resolution cryo-EM structure of a nucleosome and insight into the structure and function of the CENP-A nucleosome. The scFv approach is applicable to the structural determination of other native-like nucleosomes with distinct DNA sequences

Structure and dynamics of the active Gs-coupled human secretin receptor

The class B secretin GPCR (SecR) has broad physiological effects, with target potential for treatment of metabolic and cardiovascular disease. Molecular understanding of SecR binding and activation is important for its therapeutic exploitation. We combined cryo-electron microscopy, molecular dynamics, and biochemical cross-linking to determine a 2.3 Å structure, and interrogate dynamics, of secretin bound to the SecR:Gs complex. SecR exhibited a unique organization of its extracellular domain (ECD) relative to its 7-transmembrane (TM) core, forming more extended interactions than other family members. Numerous polar interactions formed between secretin and the receptor extracellular loops (ECLs) and TM helices. Cysteine-cross-linking, cryo-electron microscopy multivariate analysis and molecular dynamics simulations revealed that interactions between peptide and receptor were dynamic, and suggested a model for initial peptide engagement where early interactions between the far N-terminus of the peptide and SecR ECL2 likely occur following initial binding of the peptide C-terminus to the ECD

The cryo-electron microscopy supramolecular structure of the bacterial stressosome unveils its mechanism of activation

How the stressosome, the epicenter of the stress response in bacteria, transmits stress signals from the environment has remained elusive. The stressosome consists of multiple copies of three proteins RsbR, RsbS and RsbT, a kinase that is important for its activation. Using cryo-electron microscopy, we determined the atomic organization of the Listeria monocytogenes stressosome at 3.38 Å resolution. RsbR and RsbS are organized in a 60-protomers truncated icosahedron. A key phosphorylation site on RsbR (T209) is partially hidden by an RsbR flexible loop, whose "open" or "closed" position could modulate stressosome activity. Interaction between three glutamic acids in the N-terminal domain of RsbR and the membrane-bound mini-protein Prli42 is essential for Listeria survival to stress. Together, our data provide the atomic model of the stressosome core and highlight a loop important for stressosome activation, paving the way towards elucidating the mechanism of signal transduction by the stressosome in bacteria

Need for speed: Examining protein behavior during cryoEM grid preparation at different timescales

A host of new technologies are under development to improve the quality and reproducibility of cryoelectron microscopy (cryoEM) grid preparation. Here we have systematically investigated the preparation of three macromolecular complexes using three different vitrification devices (Vitrobot, chameleon, and a time-resolved cryoEM device) on various timescales, including grids made within 6 ms (the fastest reported to date), to interrogate particle behavior at the air-water interface for different timepoints. Results demonstrate that different macromolecular complexes can respond to the thin-film environment formed during cryoEM sample preparation in highly variable ways, shedding light on why cryoEM sample preparation can be difficult to optimize. We demonstrate that reducing time between sample application and vitrification is just one tool to improve cryoEM grid quality, but that it is unlikely to be a generic “silver bullet” for improving the quality of every cryoEM sample preparation

Structural basis for the initiation of eukaryotic transcription-coupled DNA repair

Eukaryotic transcription-coupled repair (TCR) is an important and well-conserved sub-pathway of nucleotide excision repair that preferentially removes DNA lesions from the template strand that block translocation of RNA polymerase II (Pol II). Cockayne syndrome group B (CSB, also known as ERCC6) protein in humans (or its yeast orthologues, Rad26 in Saccharomyces cerevisiae and Rhp26 in Schizosaccharomyces pombe) is among the first proteins to be recruited to the lesion-arrested Pol II during the initiation of eukaryotic TCR. Mutations in CSB are associated with the autosomal-recessive neurological disorder Cockayne syndrome, which is characterized by progeriod features, growth failure and photosensitivity1. The molecular mechanism of eukaryotic TCR initiation remains unclear, with several long-standing unanswered questions. How cells distinguish DNA lesion-arrested Pol II from other forms of arrested Pol II, the role of CSB in TCR initiation, and how CSB interacts with the arrested Pol II complex are all unknown. The lack of structures of CSB or the Pol II–CSB complex has hindered our ability to address these questions. Here we report the structure of the S. cerevisiae Pol II–Rad26 complex solved by cryo-electron microscopy. The structure reveals that Rad26 binds to the DNA upstream of Pol II, where it markedly alters its path. Our structural and functional data suggest that the conserved Swi2/Snf2-family core ATPase domain promotes the forward movement of Pol II, and elucidate key roles for Rad26 in both TCR and transcription elongation

Structural basis of RNA polymerase III transcription initiation.

RNA polymerase (Pol) III transcribes essential non-coding RNAs, including the entire pool of transfer RNAs, the 5S ribosomal RNA and the U6 spliceosomal RNA, and is often deregulated in cancer cells. The initiation of gene transcription by Pol III requires the activity of the transcription factor TFIIIB to form a transcriptionally active Pol III preinitiation complex (PIC). Here we present electron microscopy reconstructions of Pol III PICs at 3.4-4.0 Å and a reconstruction of unbound apo-Pol III at 3.1 Å. TFIIIB fully encircles the DNA and restructures Pol III. In particular, binding of the TFIIIB subunit Bdp1 rearranges the Pol III-specific subunits C37 and C34, thereby promoting DNA opening. The unwound DNA directly contacts both sides of the Pol III cleft. Topologically, the Pol III PIC resembles the Pol II PIC, whereas the Pol I PIC is more divergent. The structures presented unravel the molecular mechanisms underlying the first steps of Pol III transcription and also the general conserved mechanisms of gene transcription initiation

Two for one: Querying property graph databases using SPARQL via gremlinator

In the past decade Knowledge graphs have become very popular and frequently rely on the Resource Description Framework (RDF) or Property Graphs (PG) as their data models. However, the query languages for these two data models - SPARQL for RDF and the PG traversal language Gremlin - are lacking basic interoperability. In this demonstration paper, we present Gremlinator, the first translator from SPARQL - the W3C standardized language for RDF - to Gremlin - a popular property graph traversal language. Gremlinator translates SPARQL queries to Gremlin path traversals for executing graph pattern matching queries over graph databases. This allows a user, who is well versed in SPARQL, to access and query a wide variety of Graph databases avoiding the steep learning curve for adapting to a new Graph Query Language (GQL). Gremlin is a graph computing system-agnostic traversal language (covering both OLTP graph databases and OLAP graph processors), making it a desirable choice for supporting interoperability for querying Graph databases. Gremlinator is planned to be released as an Apache TinkerPop plugin in the upcoming releases

Towards an integrated graph algebra for graph pattern matching with gremlin

Graph data management has revealed beneficial characteristics in terms of flexibility and scalability by differently balancing between query expressivity and schema flexibility. This has resulted into an rapid developing new task specific graph systems, query languages and data models, such as property graphs, key-value, wide column, resource description framework (RDF), etc. Present day graph query languages are focused towards flexible graph pattern matching (aka sub-graph matching), where as graph computing frameworks aim towards providing fast parallel (distributed) execution of instructions. The consequence of this rapid growth in the variety of graph based data management systems has resulted in a lack of standardization. Gremlin, a graph traversal language and machine, provides a common platform for supporting any graph computing system (such as an OLTP graph database or OLAP graph processors). We present a formalization of graph pattern matching for Gremlin queries. We also study, discuss and consolidate various existing graph algebra operators into an integrated graph algebra