Simple Motifs Research Articles

Performance evaluation of SIFT against common image deformations on iban plaited mat motif images

Decorative plaited mat is one of the many examples of rich plait work often seen on Borneo handicraft products. The plaited mats are decorated with simple and complex motif designs; each has its own special meaning and taboos. The motif designs are used as a reflection of environment and the traditional beliefs in the Iban community. In line with efforts from UNESCO’s and Sarawak Government’s, digitization, and the use of IR4.0 technologies to preserve and promote this cultural heritage is encouraged. Towards this end goal, we present a novel image dataset containing 10 Iban plaited mat motif classes. The plaited mat motifs are made of diagonal and symmetrical shapes, as well as geometric and non-geometric patterns. Classification’s accuracy using scale-invariant feature transform (SIFT) features was evaluated against 6 common image deformations: zoom+rotation, viewpoint, image blur, JPEG compression, scale and illumination, across multiple threshold values. Varying degrees of each deformation were applied to a digitally cleaned (and cropped) image of each mat motif class. We used RANSAC to remove outliers from the noisy SIFT matching result. The optimal threshold value is 2.0e-2 with a reported 100.0% matching accuracy for the scale change and zoom+rotation set.

Interneuron-specific gamma synchronization indexes cue uncertainty and prediction errors in lateral prefrontal and anterior cingulate cortex.

Inhibitory interneurons are believed to realize critical gating functions in cortical circuits, but it has been difficult to ascertain the content of gated information for well-characterized interneurons in primate cortex. Here, we address this question by characterizing putative interneurons in primate prefrontal and anterior cingulate cortex while monkeys engaged in attention demanding reversal learning. We find that subclasses of narrow spiking neurons have a relative suppressive effect on the local circuit indicating they are inhibitory interneurons. One of these interneuron subclasses showed prominent firing rate modulations and (35-45 Hz) gamma synchronous spiking during periods of uncertainty in both, lateral prefrontal cortex (LPFC) and anterior cingulate cortex (ACC). In LPFC, this interneuron subclass activated when the uncertainty of attention cues was resolved during flexible learning, whereas in ACC it fired and gamma-synchronized when outcomes were uncertain and prediction errors were high during learning. Computational modeling of this interneuron-specific gamma band activity in simple circuit motifs suggests it could reflect a soft winner-take-all gating of information having high degree of uncertainty. Together, these findings elucidate an electrophysiologically characterized interneuron subclass in the primate, that forms gamma synchronous networks in two different areas when resolving uncertainty during adaptive goal-directed behavior.

The hammerhead self-cleaving motif as a precursor to complex endonucleolytic ribozymes.

Connections between distinct catalytic RNA motifs through networks of mutations that retain catalytic function (neutral networks) were likely central to the evolution of biocatalysis. Despite suggestions that functional RNAs collectively form an interconnected web of neutral networks, little evidence has emerged to demonstrate the existence of such intersecting networks in naturally occurring RNAs. Here we show that neutral networks of two naturally occurring, seemingly unrelated endonucleolytic ribozymes, the hammerhead (HH) and hairpin (HP), intersect. Sequences at the intersection of these networks exhibit catalytic functions corresponding to both ribozymes by potentially populating both catalytic folds and enable a smooth crossover between the two. Small and structurally simple endonucleolytic motifs like the HH ribozyme could, through mutational walks along their neutral networks, encounter novel catalytic phenotypes, and structurally flexible, bifunctional sequences at the intersection of these networks could have acted as nodes for evolutionary diversification in an RNA world. Considering the simplicity and small size of the HH ribozyme, we propose that this self-cleaving motif could have been a precursor to other more complex endonucleolytic ribozymes. More generally, our results suggest that RNAs that possess distinct sequences, structures, and catalytic functions, can potentially share evolutionary history through mutational connections in sequence space.

A stable diazoalkene

Organic Chemistry Modern organic chemistry has produced such a large array of intricately complex products that it is easy to forget the simple motifs that have eluded bulk synthesis. One such case is the diazoalkene, an unsaturated variant of the more common diazoalkanes. Consisting of three adjacent double bonds (C=C=N=N), this fragment is of particular interest as a precursor to reactive vinylidenes. Antoni et al. report the preparation of an N-heterocycle–substituted diazoalkene by oxidation of an olefinic precursor with nitrous oxide. The compound is stable in solid and solution states under inert atmosphere and reacts cleanly with isocyanides. Nat. Chem. 13 , 587 (2021).

Understanding senior's daily mobility patterns in California using human mobility motifs

Population ageing has been a thorny issue in many countries. One of the challenges is how to improve and change transportation design and transport policy development to adapt to the dramatic changes in the composition of our population. In this paper, we apply a network-based approach of human mobility measurement called “motif” to investigate the distinct patterns in daily travel for seniors (age 60 and above) in California using the 2017 National Household Travel Survey (California-NHTS) data. Motifs are networks of distinct locations visited in a day and the directional movements between them. Using patterns of motifs, we correlate the diverse daily mobility patterns with socio-demographic characteristics as well as built environment factors. We find that 15 distinct motifs can capture approximately 82% and 86% of the total senior respondents on workdays and non-workdays, respectively. Seniors are more likely to have simple motifs with three or fewer distinct locations on non-workdays, while they present more complex motifs during workdays. Given 65% of the included seniors are retired, a large number of seniors present diverse and complex daily mobility patterns instead of staying at home all day. In addition, given the similarity between the urban core, urban district, and urban neighborhood in function and spatial proximity, there is significant heterogeneity in the daily mobility patterns among seniors living in these areas. Furthermore, we find that seniors living in areas with higher percentages of single-family housing units are most likely to stay at home on workdays.

Smaller molecules crowd better: Crowder size dependence revealed by single-molecule FRET studies and depletion force modeling analysis.

The cell is an extremely crowded environment, which is known to have a profound impact on the thermodynamics, functionality, and conformational stability of biomolecules. Speculations from recent theoretical molecular dynamics studies suggest an intriguing size dependence to such purely entropic crowding effects, whereby small molecular weight crowders under constant enthalpy conditions are more effective than larger crowders on a per volume basis. If experimentally confirmed, this would be profoundly significant, as the cellular cytoplasm is also quite concentrated in smaller molecular weight solutes such as inorganic ions, amino acids, and various metabolites. The challenge is to perform such studies isolating entropic effects under isoenthalpic conditions. In this work, we first present results from single-molecule FRET spectroscopy (smFRET) on the molecular size-dependent crowding stabilization of a simple RNA tertiary motif (the GAAA tetraloop-tetraloop receptor), indeed providing evidence in support of the surprising notion in the crowding literature that "smaller is better." Specifically, systematic smFRET studies as a function of crowder solute size reveal that smaller molecules both significantly increase the RNA tertiary folding rate and, yet, simultaneously decrease the unfolding rate, predicting strongly size-dependent stabilization of RNA tertiary structures under crowded cellular conditions. The size dependence of these effects has been explored via systematic variation of crowder size over a broad range of molecular weights (90-3000 amu). Furthermore, corresponding temperature dependent studies indicate the systematic changes in the folding equilibrium to be predominantly entropic in origin, i.e., consistent with a fundamental picture of entropic molecular crowding without additional enthalpic interactions. Most importantly, all trends in the single-molecule crowding data can be quantitatively recapitulated by a simple analytic depletion force model, whereby excluded volume interactions represent the major thermodynamic driving force toward folding. Our study, thus, not only provides experimental evidence and theoretical support for small molecule crowding but also predicts further enhancement of crowding effects for even smaller molecules on a per volume basis.

A tale of two rhythms: Locked clocks and chaos in biology.

The fundamental mechanisms that control and regulate biological organisms exhibit a surprising level of complexity. Oscillators are perhaps the simplest motifs that produce time-varying dynamics and are ubiquitous in biological systems. It is also known that such biological oscillators interact with each other-for instance, circadian oscillators affect the cell cycle, and somitogenesis clock proteins in adjacent cells affect each other in developing embryos. Therefore, it is vital to understand the effects that can emerge from non-linear interaction between oscillations. Here, we show how oscillations typically arise in biology and take the reader on a tour through the great variety in dynamics that can emerge even from a single pair of coupled oscillators. We explain how chaotic dynamics can emerge and outline the methods of detecting this in experimental time traces. Finally, we discuss the potential role of such complex dynamical features in biological systems.

Prediction of Spin Density, Baird-Antiaromaticity, and Singlet-Triplet Energy Gap in Triplet-State Polybenzenoid Systems from Simple Structural Motifs.

Triplet-state aromaticity has been recently proposed as a strategy for designing functional organic electronic compounds, many of which are polycyclic aromatic systems. However, in many cases, the aromatic nature of the triplet state cannot be easily predicted. Moreover, it is often unclear how specific structural manipulations affect the electronic properties of the excited-state compounds. Herein, the relationship between the structure of polybenzenoid hydrocarbons (PBHs) and their spin-density distribution and aromatic character in the first triplet excited state is studied. Although a direct link is not immediately visible, classifying the PBHs according to their annulation sequence reveals regularities. Based on these, a set of guidelines is defined to qualitatively predict the location of spin and paratropicity and the singlet-triplet energy gap in larger PBHs, using only their smaller tri- and tetracyclic components, and subsequently tested on larger systems.

Cover Feature: Prediction of Spin Density, Baird‐Antiaromaticity, and Singlet–Triplet Energy Gap in Triplet‐State Polybenzenoid Systems from Simple Structural Motifs (Chem. Eur. J. 23/2021)

Structure, sequence, spin: The structures of polybenzenoid hydrocarbons are analyzed in terms of the sequence of tricyclic annulations, revealing regularities in the location of spin density and Baird-antiaromaticity. The two properties localize onto specific tri- and tetracyclic substructures according to a hierarchy: linear, zig-zag, curved. The same preferences are reflected in the relative energy of the T1 systems and in the singlet-triplet energy gaps. More information can be found in the Full Paper by R. Gershoni-Poranne et al. on page 6923.

Geometrical manipulation of complex supramolecular tessellations by hierarchical assembly of amphiphilic platinum(II) complexes.

Here we report complex supramolecular tessellations achieved by the directed self-assembly of amphiphilic platinum(II) complexes. Despite the twofold symmetry, these geometrically simple molecules exhibit complicated structural hierarchy in a columnar manner. A possible key to such an order increase is the topological transition into circular trimers, which are noncovalently interlocked by metal···metal and π-π interactions, thereby allowing for cofacial stacking in a prismatic assembly. Another key to success is to use the immiscibility of the tailored hydrophobic and hydrophilic sidechains. Their phase separation leads to the formation of columnar crystalline nanostructures homogeneously oriented on the substrate, featuring an unusual geometry analogous to a rhombitrihexagonal Archimedean tiling. Furthermore, symmetry lowering of regular motifs by design results in an orthorhombic lattice obtained by the coassembly of two different platinum(II) amphiphiles. These findings illustrate the potentials of supramolecular engineering in creating complex self-assembled architectures of soft materials.

Modified Cyclodextrins Solubilize Elemental Sulfur in Water and Enable Biological Sulfane Sulfur Delivery

An important form of biological sulfur is sulfane sulfur, or S0, which is found in polysulfide and persulfide compounds as well as in elemental sulfur. Sulfane sulfur, often in the form of S8, functions as a key energy source in the metabolic processes of thermophilic Archaean organisms found in sulfur-rich environments and can be metabolized both aerobically and anaerobically by different archaeons. Despite this importance, S8 has a low solubility in water (∼19 nM), raising questions of how it can be made chemically accessible in complex environments. Motivated by prior crystallographic data showing S8 binding to hydrophobic motifs in filamentous glycoproteins from the sulfur reducing Staphylothermus marinus anaerobe, we demonstrate that simple macrocyclic hydrophobic motifs, such as 2-hydroxypropyl β-cyclodextrin (2HPβ), are sufficient to solubilize S8 at concentrations up to 2.0 ± 0.2 mM in aqueous solution. We demonstrate that the solubilized S8 can be reduced with the common reductant tris(2-carboxyethyl)phosphine (TCEP) and reacts with thiols to generate H2S. The thiol-mediated conversion of 2HPβ/S8 to H2S ranges from 80% to quantitative efficiency for Cys and glutathione (GSH). Moreover, we demonstrate that 2HPβ can catalyze the Cys-mediated reduction of S8 to H2S in water. Adding to the biological relevance of the developed systems, we demonstrate that treatment of Raw 264.7 macrophage cells with the 2HPβ/S8 complex prior to LPS stimulation decreases NO2− levels, which is consistent with known activities of bioavailable H2S and sulfane sulfur. Taken together, these investigations provide a new strategy for delivering H2S and sulfane sulfur in complex systems and more importantly provide new insights into the chemical accessibility and storage of S0 and S8 in biological environments.

Transcription Factor Binding Affinities and DNA Shape Readout.

SummaryAn essential event in gene regulation is the binding of a transcription factor (TF) to its target DNA. Models considering the interactions between the TF and the DNA geometry proved to be successful approaches to describe this binding event, while conserving data interpretability. However, a direct characterization of the DNA shape contribution to binding is still missing due to the lack of accurate and large-scale binding affinity data. Here, we use a binding assay we recently established to measure with high sensitivity the binding specificities of 13 Drosophila TFs, including dinucleotide dependencies to capture non-independent amino acid-base interactions. Correlating the binding affinities with all DNA shape features, we find that shape readout is widely used by these factors. A shape readout/TF-DNA complex structure analysis validates our approach while providing biological insights such as positively charged or highly polar amino acids often contact nucleotides that exhibit strong shape readout.

Self-assembly of bioinspired and biologically functional materials

Abstract

Small-residue packing motifs modulate the structure and function of a minimal de novo membrane protein

Alpha-helical integral membrane proteins contain conserved sequence motifs that are known to be important in helix packing. These motifs are a promising starting point for the construction of artificial proteins, but their potential has not yet been fully explored. Here, we study the impact of introducing a common natural helix packing motif to the transmembrane domain of a genetically-encoded and structurally dynamic de novo membrane protein. The resulting construct is an artificial four-helix bundle with lipophilic regions that are defined only by the amino acids L, G, S, A and W. This minimal proto-protein could be recombinantly expressed by diverse prokaryotic and eukaryotic hosts and was found to co-sediment with cellular membranes. The protein could be extracted and purified in surfactant micelles and was monodisperse and stable in vitro, with sufficient structural definition to support the rapid binding of a heme cofactor. The reduction in conformational diversity imposed by this design also enhances the nascent peroxidase activity of the protein-heme complex. Unexpectedly, strains of Escherichia coli expressing this artificial protein specifically accumulated zinc protoporphyrin IX, a rare cofactor that is not used by natural metalloenzymes. Our results demonstrate that simple sequence motifs can rigidify elementary membrane proteins, and that orthogonal artificial membrane proteins can influence the cofactor repertoire of a living cell. These findings have implications for rational protein design and synthetic biology.

Syntheses and crystal structures of solvate complexes of alkaline earth and lanthanoid metal iodides with N,N-dimethylformamide

Abstract The solvate complexes that can be obtained by either dissolving metal iodides in N,N-dimethylformamide (DMF) or by synthesising them in DMF have the general composition [M(DMF) x ]I y . DMF shows to behave as simple monodentate ligand with low sterical impact, so that x in the composition follows the radius of M y+. We present here the crystal structures of the alkaline earth and lanthanoid metal iodide complexes [Mg(DMF)6]I2, [Ca(DMF)6]I2, [Sr(DMF)7]I2, [Ba(DMF)8]I2, [La(DMF)9]I3, [Ln(DMF)8]I3 (isotypic series for Ln = Nd, Sm, Eu, Dy, Gd, Er, Yb and Lu) and for the tris-triiodide complex salt [Sc(DMF)6](I3)3. Their different crystal structure types can be compared on the basis of the packing topologies of the nearly spherical cationic entities which show simple sphere packing motifs.

Reconfigurable T-junction DNA Origami.

DNA self-assembly allows the construction of nanometre-scale structures and devices. Structures with thousands of unique components are routinely assembled in good yield. Experimental progress has been rapid, based largely on empirical design rules. Herein, we demonstrate a DNA origami technique designed as a model system with which to explore the mechanism of assembly. The origami fold is controlled through single-stranded loops embedded in a double-stranded DNA template and is programmed by a set of double-stranded linkers that specify pairwise interactions between loop sequences. Assembly is via T-junctions formed by hybridization of single-stranded overhangs on the linkers with the loops. The sequence of loops on the template and the set of interaction rules embodied in the linkers can be reconfigured with ease. We show that a set of just two interaction rules can be used to assemble simple T-junction origami motifs and that assembly can be performed at room temperature.

Genetic variability in Rubus ellipticus collections assessed by morphological traits and EST-SSR markers

Rubus ellipticus Smith. commonly known as ‘Yellow Himalayan raspberry’ is an important member of Rosaceae family with high medicinal importance having antioxidant and antibacterial properties. This study was done with the objective of characterizing 21 R. ellipticus collections from different regions of India, based on morphological descriptors and expressed sequence tags-simple sequence repeat (EST-SSR) markers. Broad phenotypic variability among the R. ellipticus collections was detected by using morphological descriptors. The Euclidian distance matrix discriminated two groups, based on morphological characters. A set of 68 EST-SSR markers were developed based on 7777 unigenes generated by us from ‘Kumarhatti-1’ collection of R. ellipticus using assembled pair—end sequences from Illumina NextSeq 500. The ESTs containing simple sequence repeat motifs were extracted using Microsatellite identification tool and primers were designed. Out of 68 EST-SSRs polymorphism was detected using 61 (89.7%) primer pairs, indicating high genetic variability in the R. ellipticus collections. Effective multiplex ratio, marker index and polymorphism information content were 0.43, 0.24 and 0.50, respectively. The unweighted pair group method with arithmetic mean coincided with the bootstrap analysis and two groups were formed, separating the collections Uttrakhand from the other. Morphological descriptors along with EST-SSR markers proved efficient in detecting the levels of genetic variability among the collections maintained in the field. These results can be used as an additional source of exploitation in R. ellipticus breeding programs.

Direct Identification of Amyloid Peptide Fragments in Human α-Synuclein Based on Consecutive Hydrophobic Amino Acids.

Formation of amyloid fibrils by misfolding α-synuclein is a characteristic feature of Parkinson’s disease, but the exact molecular mechanism of this process has long been an unresolved mystery. Identification of critical amyloid peptide fragments from α-synuclein may hold the key to decipher this mystery. Focusing on consecutive hydrophobic amino acids (CHAA) in the protein sequence, in this study we proposed a sequence-based strategy for direct identification of amyloid peptide fragments in α-synuclein. We picked out three CHAA fragments (two hexapeptides and one tetrapeptide) from α-synuclein and studied their amyloidogenic property. The thioflavin-T binding test, transmission electron microscopy, Congo red staining, and Fourier transform infrared spectroscopy revealed that although only hexapeptides could undergo amyloid aggregation on their own, extended peptide fragments based on any of the three peptides could form typical amyloid fibrils. Primary amyloidogenic fragments based on the three peptides showed synergetic aggregation behavior and could accelerate the aggregation of full-length α-synuclein. It was proved that hydrophobic interaction played a predominant role for the aggregation of these peptides and full-length α-synuclein. A central alanine-to-lysine substitution in each hydrophobic fragment completely eliminated the peptides’ amyloidogenic property, and alanine-to-lysine substitutions at corresponding sites in full-length α-synuclein also decreased the protein’s amyloidogenic potency. These findings suggested that CHAA fragments were potentially amyloidogenic and played an important role for the aggregation of α-synuclein. The identification of these fragments might provide helpful information for eventually clarifying the molecular mechanism of α-synuclein aggregation. On the other hand, our study suggested that the CHAA fragment might be a simple motif for direct sequence-based identification of amyloid peptides.

The Voices of Others: Intertextuality and Authorial Presences in Jean Rhys's Short Fiction

My project here is to discuss the extent of Rhys's permeability to the voices of ‘others’, especially when it comes to quoting, inserting, using, or elaborating her own writing with a recourse to the literary authority of other writers. The postcolonial concept of ‘writing back’ obliterates the process of actual writing to the profit of the Western-constructed idea of an accusatory pattern in the literary agendas of authors from former Empires. As critical as Rhys might have been of European colonialism, a limitation of her work to a gesture of ‘writing back’ amounts to denying the polyphony orchestrated by the writer, thereby blurring any form of aesthetic purpose per se. Therefore, in an attempt to avoid a strictly postcolonial discourse, my article studies the wide scope of examples of intertextuality in Jean Rhys's short fiction (mainly in the short stories ‘Let Them Call It Jazz’, ‘Hunger’, ‘La Grosse Fifi’, ‘Invitation to the Dance’ and ‘Temps Perdi’), in relation to the very notions of authority—both the author's, and her peers’. What is more, ‘others’ are present in her writing under the form of absent voices piercing through the fabric of the text, which results in a failure to locate the main source of authority. I shall enquire into the notion of failure as writing and reading aesthetics, rather than a simple literary motif.

Chemical Reaction Networks Possess Intrinsic, Temperature-Dependent Functionality.

Temperature influences the life of many organisms in various ways. A great number of organisms live under conditions where their ability to adapt to changes in temperature can be vital and largely determines their fitness. Understanding the mechanisms and principles underlying this ability to adapt can be of great advantage, for example, to improve growth conditions for crops and increase their yield. In times of imminent, increasing climate change, this becomes even more important in order to find strategies and help crops cope with these fundamental changes. There is intense research in the field of acclimation that comprises fluctuations of various environmental conditions, but most acclimation research focuses on regulatory effects and the observation of gene expression changes within the examined organism. As thermodynamic effects are a direct consequence of temperature changes, these should necessarily be considered in this field of research but are often neglected. Additionally, compensated effects might be missed even though they are equally important for the organism, since they do not cause observable changes, but rather counteract them. In this work, using a systems biology approach, we demonstrate that even simple network motifs can exhibit temperature-dependent functional features resulting from the interplay of network structure and the distribution of activation energies over the involved reactions. The demonstrated functional features are (i) the reversal of fluxes within a linear pathway, (ii) a thermo-selective branched pathway with different flux modes and (iii) the increased flux towards carbohydrates in a minimal Calvin cycle that was designed to demonstrate temperature compensation within reaction networks. Comparing a system’s response to either temperature changes or changes in enzyme activity we also dissect the influence of thermodynamic changes versus genetic regulation. By this, we expand the scope of thermodynamic modelling of biochemical processes by addressing further possibilities and effects, following established mathematical descriptions of biophysical properties.