SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: System

168

BACKGROUND: Genotyping and massively-parallel sequencing projects result in a vast amount of diploid data that is only rarely resolved into its constituent haplotypes. It is nevertheless this phased information that is transmitted from one generation to the next and is most directly associated with biological function and the genetic causes of biological effects. Despite progress made in genome-wide sequencing and phasing algorithms and methods, problems assembling (and reconstructing linear haplotypes in) regions of repetitive DNA and structural variation remain. These dynamic and structurally complex regions are often poorly understood from a sequence point of view. Regions such as these that are highly similar in their sequence tend to be collapsed onto the genome assembly. This is turn means downstream determination of the true sequence haplotype in these regions poses a particular challenge. For structurally complex regions, a more focussed approach to assembling haplotypes may be required. RESULTS: In order to investigate reconstruction of spatial information at structurally complex regions, we have used an emulsion haplotype fusion PCR approach to reproducibly link sequences of up to 1kb in length to allow phasing of multiple variants from neighbouring loci, using allele-specific PCR and sequencing to detect the phase. By using emulsion systems linking flanking regions to amplicons within the CNV, this led to the reconstruction of a 59kb haplotype across the DEFA1A3 CNV in HapMap individuals. CONCLUSION: This study has demonstrated a novel use for emulsion haplotype fusion PCR in addressing the issue of reconstructing structural haplotypes at multiallelic copy variable regions, using the DEFA1A3 locus as an example.

Concepts: DNA, Genetics, Molecular biology, Sequence, System, Reconstruction era of the United States, Haplotype, International HapMap Project

161

Designing RNAs that form specific secondary structures is enabling better understanding and control of living systems through RNA-guided silencing, genome editing and protein organization. Little is known, however, about which RNA secondary structures might be tractable for downstream sequence design, increasing the time and expense of design efforts due to inefficient secondary structure choices. Here, we present insights into specific structural features that increase the difficulty of finding sequences that fold into a target RNA secondary structure, summarizing the design efforts of tens of thousands of human participants and three automated algorithms (RNAInverse, INFO-RNA and RNA-SSD) in the Eterna massive open laboratory. Subsequent tests through three independent RNA design algorithms (NUPACK, DSS-Opt and MODENA) confirmed the hypothesized importance of several features in determining design difficulty, including sequence length, mean stem length, symmetry and specific difficult-to-design motifs such as zigzags. Based on these results, we have compiled an Eterna100 benchmark of 100 secondary structure design challenges that span a large range in design difficulty to help test future efforts. Our in silico results suggest new routes for improving computational RNA design methods and for extending these insights to assess “designability” of single RNA structures, as well as of switches for in vitro and in vivo applications.

Concepts: Protein, Genome, RNA, Secondary structure, Structure, In vivo, In vitro, System

144

More than 35 years and 11 000 publications after the discovery of quasicrystals by Dan Shechtman, quite a bit is known about their occurrence, formation, stability, structures and physical properties. It has also been discovered that quasiperiodic self-assembly is not restricted to intermetallics, but can take place in systems on the meso- and macroscales. However, there are some blank areas, even in the centre of the big picture. For instance, it has still not been fully clarified whether quasicrystals are just entropy-stabilized high-temperature phases or whether they can be thermodynamically stable at 0 K as well. More studies are needed for developing a generally accepted model of quasicrystal growth. The state of the art of quasicrystal research is briefly reviewed and the main as-yet unanswered questions are addressed, as well as the experimental limitations to finding answers to them. The focus of this discussion is on quasicrystal structure analysis as well as on quasicrystal stability and growth mechanisms.

Concepts: Structure, Model theory, System, Need, Centrifugation, Quasicrystal, Quasiperiodicity, Dan Shechtman

136

Dragonfly has excellent flight performance and maneuverability due to the complex vein structure of wing. In this research, nodus as an important structural element of the dragonfly wing is investigated through an experimental visualization approach. Three vein structures were fabricated as, open-nodus structure, closed-nodus structure (with a flex-limiter) and rigid wing. The samples were conducted in a wind tunnel with a high speed camera to visualize the deformation of wing structure in order to study the function of nodus structured wing in gliding flight. According to the experimental results, nodus has a great influence on the flexibility of the wing structure. Moreover, the closed-nodus wing (with a flex-limiter) enables the vein structure to be flexible without losing the strength and rigidity of the joint. These findings enhance the knowledge of insect-inspired nodus structured wing and facilitate the application of Micro Air Vehicle (MAV) in gliding flight.

Concepts: Structure, Aerodynamics, System, Flight, Wing, Flying and gliding animals, Aircraft, Bird flight

104

The Palaeogene Ardnamurchan central igneous complex, NW Scotland, was a defining place for the development of the classic concepts of cone-sheet and ring-dyke emplacement and has thus fundamentally influenced our thinking on subvolcanic structures. We have used the available structural information on Ardnamurchan to project the underlying three-dimensional (3D) cone-sheet structure. Here we show that a single elongate magma chamber likely acted as the source of the cone-sheet swarm(s) instead of the traditionally accepted model of three successive centres. This proposal is supported by the ridge-like morphology of the Ardnamurchan volcano and is consistent with the depth and elongation of the gravity anomaly underlying the peninsula. Our model challenges the traditional model of cone-sheet emplacement at Ardnamurchan that involves successive but independent centres in favour of a more dynamical one that involves a single, but elongate and progressively evolving magma chamber system.

Concepts: Structure, Earth, Igneous rock, System, Magma, Basalt, Volcanology, Caldera

81

The science of consciousness has made great strides by focusing on the behavioural and neuronal correlates of experience. However, while such correlates are important for progress to occur, they are not enough if we are to understand even basic facts, for example, why the cerebral cortex gives rise to consciousness but the cerebellum does not, though it has even more neurons and appears to be just as complicated. Moreover, correlates are of little help in many instances where we would like to know if consciousness is present: patients with a few remaining islands of functioning cortex, preterm infants, non-mammalian species and machines that are rapidly outperforming people at driving, recognizing faces and objects, and answering difficult questions. To address these issues, we need not only more data but also a theory of consciousness-one that says what experience is and what type of physical systems can have it. Integrated information theory (IIT) does so by starting from experience itself via five phenomenological axioms: intrinsic existence, composition, information, integration and exclusion. From these it derives five postulates about the properties required of physical mechanisms to support consciousness. The theory provides a principled account of both the quantity and the quality of an individual experience (a quale), and a calculus to evaluate whether or not a particular physical system is conscious and of what. Moreover, IIT can explain a range of clinical and laboratory findings, makes a number of testable predictions and extrapolates to a number of problematic conditions. The theory holds that consciousness is a fundamental property possessed by physical systems having specific causal properties. It predicts that consciousness is graded, is common among biological organisms and can occur in some very simple systems. Conversely, it predicts that feed-forward networks, even complex ones, are not conscious, nor are aggregates such as groups of individuals or heaps of sand. Also, in sharp contrast to widespread functionalist beliefs, IIT implies that digital computers, even if their behaviour were to be functionally equivalent to ours, and even if they were to run faithful simulations of the human brain, would experience next to nothing.

Concepts: Neuron, Brain, Mathematics, Human brain, Cerebral cortex, Cerebellum, Consciousness, System

74

This article investigates the factors that escalate competition into dangerous conflict. Recent sociological theorizing claims that such escalations are particularly likely in dyads of structurally equivalent people (i.e., actors who have the same relations with the same third parties). Using panel data on Formula One races from 1970 through 2014, we model the probability that two drivers collide on the racetrack (an observable trace of conflict) as a function of their structural equivalence in a dynamic network of competitive relationships. Our main hypothesis, that the likelihood of conflict rises with structural equivalence, receives empirical support. Our findings also show that the positive association between structural equivalence and conflict is neither merely a matter of contention for official position nor an artifact of inherently hostile parties spatially exposed to each other. Our analyses further reveal that this positive association is concentrated in a number of theoretically predictable conditions: among age-similar dyads, among stronger performers, in stable competitive networks, and in safe, rather than dangerous, weather conditions. Implications for future research on conflict, networks, and tournaments are discussed.

Concepts: Scientific method, Quantum mechanics, Competition, Structure, System, Organization, Equivalence, Tournament

73

Obtaining high-resolution information from a complex system, while maintaining the global perspective needed to understand system function, represents a key challenge in biology. Here we address this challenge with a method (termed CLARITY) for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable. Using mouse brains, we show intact-tissue imaging of long-range projections, local circuit wiring, cellular relationships, subcellular structures, protein complexes, nucleic acids and neurotransmitters. CLARITY also enables intact-tissue in situ hybridization, immunohistochemistry with multiple rounds of staining and de-staining in non-sectioned tissue, and antibody labelling throughout the intact adult mouse brain. Finally, we show that CLARITY enables fine structural analysis of clinical samples, including non-sectioned human tissue from a neuropsychiatric-disease setting, establishing a path for the transmutation of human tissue into a stable, intact and accessible form suitable for probing structural and molecular underpinnings of physiological function and disease.

Concepts: DNA, Molecular biology, Blood, Biology, Histology, System, Immunohistochemistry, Staining

60

The rapid spread of Zika virus (ZIKV), which causes microcephaly and Guillain-Barré syndrome, signals an urgency to identify therapeutics. Recent efforts to rescreen dengue virus human antibodies for ZIKV cross-neutralization activity showed antibody C10 as one of the most potent. To investigate the ability of the antibody to block fusion, we determined the cryoEM structures of the C10-ZIKV complex at pH levels mimicking the extracellular (pH8.0), early (pH6.5) and late endosomal (pH5.0) environments. The 4.0 Å resolution pH8.0 complex structure shows that the antibody binds to E proteins residues at the intra-dimer interface, and the virus quaternary structure-dependent inter-dimer and inter-raft interfaces. At pH6.5, antibody C10 locks all virus surface E proteins, and at pH5.0, it locks the E protein raft structure, suggesting that it prevents the structural rearrangement of the E proteins during the fusion event-a vital step for infection. This suggests antibody C10 could be a good therapeutic candidate.

Concepts: Antibody, Protein, Protein structure, Acid, Blood, Structure, PH, System

55

Tensegrity structures with detached struts are naturally suitable for deployable applications, both in terrestrial and outer-space structures, as well as morphing devices. Composed of discontinuous struts and continuous cables, such systems are only structurally stable when self-stress is induced; otherwise, they lose the original geometrical configuration (while keeping the topology) and thus can be tightly packed. We exploit this feature by using stimulus responsive polymers to introduce a paradigm for creating actively deployable 3D structures with complex shapes. The shape-change of 3D printed smart materials adds an active dimension to the configurational space of some structural components. Then we achieve dramatic global volume expansion by amplifying component-wise deformations to global configurational change via the inherent deployability of tensegrity. Through modular design, we can generate active tensegrities that are relatively stiff yet resilient with various complexities. Such unique properties enable structural systems that can achieve gigantic shape change, making them ideal as a platform for super light-weight structures, shape-changing soft robots, morphing antenna and RF devices, and biomedical devices.

Concepts: Structure, Systems, System, Shapeshifting