bluuebunny/crossref_metadata_2025 huggingface dataset:
Self-assembly of the butterfly proboscis: the role of capillary forces
Authors: Zhang Chengqi , Adler Peter H. , Monaenkova Daria , Andrukh Taras , Pometto Suellen , Beard Charles E. , Kornev Konstantin G.
Published: July 2018

The proboscis of butterflies and moths consists of two C-shaped fibres, the galeae, which are united after the insect emerges from the pupa. We observed that proboscis self-assembly is facilitated by discharge of saliva. In contrast with vertebrate saliva, butterfly saliva is not slimy and is an almost inviscid, water-like fluid. Butterfly saliva, therefore, cannot offer any viscoelastic adhesiveness. We hypothesized that capillary forces are responsible for helping butterflies and moths pull and hold their galeae together while uniting them mechanically. Theoretical analysis supported by X-ray micro-computed tomography on columnar liquid bridges suggests that both concave and convex liquid bridges are able to pull the galeae together. Theoretical and experimental analyses of capillary forces acting on natural and artificial proboscises show that these forces are sufficiently high to hold the galeae together.
Flat and microstructured polymeric membranes in organs-on-chips
Authors: Pasman Thijs , Grijpma Dirk , Stamatialis Dimitrios , Poot Andreas
Published: July 2018

In recent years, organs-on-chips (OOCs) have been developed to meet the desire for more realistic
in vitro
cell culture models. These systems introduce microfluidics, mechanical stretch and other physiological stimuli to
in vitro
models, thereby significantly enhancing their descriptive power. In most OOCs, porous polymeric membranes are used as substrates for cell culture. The polymeric material, morphology and shape of these membranes are often suboptimal, despite their importance for achieving ideal cell functionality such as cell–cell interaction and differentiation. The currently used membranes are flat and thus do not account for the shape and surface morphology of a tissue. Moreover, the polymers used for fabrication of these membranes often lack relevant characteristics, such as mechanical properties matching the tissue to be developed and/or cytocompatibility. Recently, innovative techniques have been reported for fabrication of porous membranes with suitable porosity, shape and surface morphology matching the requirements of OOCs. In this paper, we review the state of the art for developing these membranes and discuss their application in OOCs.
Multilayer stag beetle elytra perform better under external loading via non-symmetric bending properties
Authors: Kundanati Lakshminath , Signetti Stefano , Gupta Himadri S. , Menegon Michele , Pugno Nicola M.
Published: July 2018

Insect cuticle has drawn a lot of attention from engineers because of its multifunctional role in the life of insects. Some of these cuticles have an optimal combination of lightweight and good mechanical properties, and have inspired the design of composites with novel microstructures. Among these, beetle elytra have been explored extensively for their multilayered structure, multifunctional roles and mechanical properties. In this study, we investigated the bending properties of elytra by simulating their natural loading condition and comparing it with other loading configurations. Further, we examined the properties of their constitutive bulk layers to understand the contribution of each one to the overall mechanical behaviour. Our results showed that elytra are graded, multilayered composite structures that perform better in natural loading direction in terms of both flexural modulus and strength which is likely an adaptation to withstand loads encountered in the habitat. Experiments are supported by analytical calculations and finite element method modelling, which highlighted the additional role of the relatively stiff external exocuticle and of the flexible thin bottom layer in enhancing flexural mechanical properties. Such studies contribute to the knowledge of the mechanical behaviour of this natural composite material and to the development of novel bioinspired multifunctional composites and for optimized armours.
Bayesian inference of antigenic and non-antigenic variables from haemagglutination inhibition assays for influenza surveillance
Authors: Adabor Emmanuel S. , Ndifon Wilfred
Published: July 2018

Haemagglutination inhibition (HI) assays are typically used for comparing and characterizing influenza viruses. Data obtained from the assays (titres) are used quantitatively to determine antigenic differences between influenza strains. However, the use of these titres has been criticized as they sometimes fail to capture accurate antigenic differences between strains. Our previous analytical work revealed how antigenic and non-antigenic variables contribute to the titres. Building on this previous work, we have developed a Bayesian method for decoupling antigenic and non-antigenic contributions to the titres in this paper. We apply this method to a compendium of HI titres of influenza A (H3N2) viruses curated from 1968 to 2016. Remarkably, the results of this fit indicate that the non-antigenic variable, which is inversely correlated with viral avidity for the red blood cells used in HI assays, oscillates during the course of influenza virus evolution, with a period that corresponds roughly to the timescale on which antigenic variants replace each other. Together, the results suggest that the new Bayesian method is applicable to the analysis of long-term dynamics of both antigenic and non-antigenic properties of influenza virus.
Walking together: behavioural signatures of psychological crowds
Authors: Templeton Anne , Drury John , Philippides Andrew
Published: July 2018

Research in crowd psychology has demonstrated key differences between the behaviour of
physical
crowds where members are in the same place at the same time, and the collective behaviour of
psychological
crowds where the entire crowd perceive themselves to be part of the same group through a shared social identity. As yet, no research has investigated the behavioural effects that a shared social identity has on crowd movement at a pedestrian level. To investigate the direction and extent to which social identity influences the movement of crowds, 280 trajectories were tracked as participants walked in one of two conditions: (1) a psychological crowd primed to share a social identity; (2) a naturally occurring physical crowd. Behaviour was compared both within and between the conditions. In comparison to the physical crowd, members of the psychological crowd (i) walked slower, (ii) walked further, and (iii) maintained closer proximity. In addition, pedestrians who had to manoeuvre around the psychological crowd behaved differently to pedestrians who had to manoeuvre past the naturally occurring crowd. We conclude that the behavioural differences between physical and psychological crowds must be taken into account when considering crowd behaviour in event safety management and computer models of crowds.
Donor–acceptor Stenhouse adduct-grafted polycarbonate surfaces: selectivity of the reaction for secondary amine on surface
Authors: Singh Sukhdeep , Mai Patrick , Borowiec Justyna , Zhang Yixin , Lei Yong , Schober Andreas
Published: July 2018

Donor–acceptor Stenhouse adducts (DASAs) are gaining attention from organic and material chemists due to their visible light-stimulated photochromic properties. In this report, we present a facile method for grafting coloured triene on polycarbonate surface, without involving any pre-treatments like plasma activation, etc. The chemoselectivity of carbonate with a primary amine and Meldrum's activated furan (MAF) with polymer bound secondary amine has been exploited to graft photoswitchable DASA on the polymer surface. Primary, secondary and tertiary amine-functionalized polycarbonate surfaces have been prepared to evaluate the reactivity of amine with MAF.
Rheological properties and damage-control mechanism of oil-based drilling fluid with different types of weighting agents
Authors: Xu Peng , Xu Mingbiao , Tao Zhengwu , Wang Zhihong , Huang Ting
Published: July 2018

The great amount of solid particles contained in a weighting agent is a major cause of the problems in both rheology properties and damage control mechanism of an oil-based drilling fluid (OBM). Therefore, a proper type of weighting agent can be a solution for the application of OBM. In this study, three weighting agents that have been commonly used with OBM, namely, standard barite, submicron barite and superfine manganese ore, are studied. Rheological properties of OBM and the degree of formation damage are assessed with regard to the three weighting agents. The agents are also studied in aspects of particle size, micromorphology, filtration loss and wall-building property, acid dissolution efficiency of mud cake, lubricity and sedimentation stability to analyse the effects of the agents on rheological properties and the degree of damage as well as to figure out the mechanism of rheology control and damage control. For the OBM, there is a mutual effect between rheological stability and the degree of damage. In consideration of the agents' properties, we can enhance the rheological stability of the OBM and control the degree of formation damage by properly selecting particle size, using acid-soluble materials and forming the mud cake with ultra-low permeability that can easily be cleared away.
N
,
N
-chelated nickel catalysts for highly branched polyolefin elastomers: a survey
Authors: Mahmood Qaiser , Sun Wen-Hua
Published: July 2018

The physical properties and end applications of polyolefin materials are defined by their chain architectures and topologies. These properties can, in part, be controlled by a judicious choice of the steric and electronic properties of the catalyst and, in particular, the ligand framework. One major achievement in this field is the discovery of thermoplastic polyolefin elastomers that combine the processing and recyclable characteristics of thermoplastics with the flexibility and ductility of elastomers. These polymers are highly sought after as alternative materials to thermoset elastomers. In this perspective, works in the literature related to the development of nickel catalysts as well as their implementations for the synthesis of polyolefin elastomers are summarized in detail. Throughout the perspective, attention has been focused on developing the relationship between catalyst structure and performance, on strategies for the synthesis of polyolefin elastomer using nickel catalysts, on properties of the resultant polyolefin, such as degree of branching and crystallinity, as well as on their effects on mechanical properties. The future perspective regarding the most recent developments in single-step production of polyethylene elastomers will also be presented.
Aerofoil optimization for improving the power performance of a vertical axis wind turbine using multiple streamtube model and genetic algorithm
Authors: Liang Changping , Li Huaxing
Published: July 2018

This paper reports on the optimization of the NACA0015 aerofoil for improving the power performance of a vertical axis wind turbine (VAWT). The target range of the chord
Re
is 3 × 10
5
–10
6
, the tip speed ratio (TSR) is 2–6 and the solidity is 0.2–0.6. This aerofoil is widely applied in small-scale VAWTs. In the optimization process, in which the class and shape function transformation parametrization method was used to perturb the aerofoil geometry, the thickness and camber of the aerofoil were selected as the constraints and the value of the maximum tangential force coefficient was chosen as the objective function. The aerodynamic performance of the aerofoil was calculated by combining the XFOIL program and Viterna–Corrigan post-stall model, while the aerofoil's performance was validated with computational fluid dynamic simulations. The results illustrated that, compared to an unoptimized NACA0015 aerofoil, the optimized aerofoil's lift to drag ratio was improved over a wide range of attack angles and the stall performance was gentler. The maximum lift coefficient, the maximum lift to drag ratio and the maximum tangential force coefficient were increased by 7.5%, 9% and 8.87%, respectively. Finally, this paper predicted the rotor efficiency with both the unoptimized and optimized NACA0015 aerofoils for different TSRs and different solidities using the multiple streamtube model. The results showed that the rotor with the optimized aerofoil has a higher efficiency.
Structural, elastic, mechanical and thermodynamic properties of HfB
4
under high pressure
Authors: Chang Jing , Zhou Xiaolin , Liu Ke , Ge Nina
Published: July 2018

The present work aims to study the structural, elastic, mechanical and thermodynamic properties of the newly discovered orthorhombic
Cmcm
structure HfB
4
(denoted as
Cmcm
-HfB
4
hereafter) under pressure by the first-principles calculations. The obtained equilibrium structure parameters and ground-state mechanical properties were in excellent agreement with the other theoretical results. The calculated elastic constants and phonon dispersion spectra show that
Cmcm
-HfB
4
is mechanically and dynamically stable up to 100 GPa and no phase transition was observed. An analysis of the elastic modulus indicates that
Cmcm
-HfB
4
possesses a large bulk modulus, shear modulus and Young's modulus. The superior mechanical properties identify this compound as a possible candidate for a superhard material. Further hardness calculation confirmed that this compound is a superhard material with high hardness (45.5 GPa for GGA); and the relatively strong B–B covalent bonds’ interaction and the planar six-membered ring boron network in
Cmcm
-HfB
4
are crucial for the high hardness. Additionally, the pressure-induced elastic anisotropy behaviour has been analysed by several different anisotropic indexes. By calculating the
B
/
G
and Poisson's ratio, it is predicted that
Cmcm
-HfB
4
possesses brittle behaviour in the range of pressure from 0 to 100 GPa, and higher pressures can reduce its brittleness. Finally, the thermodynamic properties, including enthalpy (Δ
H
), free energy (Δ
G
), entropy (Δ
S
), heat capacity (

C
V

) and Debye temperature (

Θ
D

) are obtained under pressure and temperature, and the results are also interpreted.
Storage stability of organophosphorus pesticide residues in peanut and soya bean extracted solutions
Authors: Guo Gang , Jiang Naiwen , Liu Fengmao , Bian Yanli
Published: July 2018

This study was performed to determine the storage stability of organophosphorus pesticide residues in high oil content commodity matrices, peanut and soya bean. The storage conditions included different types of solvents (ethyl acetate, acetone and hexane) and corresponding extracted matrix solutions, light and temperature. It was found that three pesticides degraded quickly especially in ethyl acetate solvent. They decreased greater than 30% when stored for 3 days at −20°C in ethyl acetate; the results showed that the stability could be improved in the extracted matrix solutions. Light had a slight effect for stability of phorate and fenthion, while it played an important effect for disulfoton with the exception of ethyl acetate as solvent. Even at −20°C, exposure to solvents or extracted matrix solution resulted in 40.67, 96.33 and 35.07% loss of phorate, disulfoton and fenthion. Hence, it could be assumed that these three residues could be more stable at lower temperature, in the dark and in acetone or hexane extracted peanut and soya bean solutions.
Heterochromatin-enriched assemblies reveal the sequence and organization of theDrosophila melanogasterY chromosome
Authors: Chang Ching-Ho , Larracuente Amanda M.
Published: July 2018

Heterochromatic regions of the genome are repeat-rich and gene poor, and are therefore underrepresented in even in the best genome assemblies. One of the most difficult regions of the genome to assemble are sex-limited chromosomes. TheDrosophila melanogasterY chromosome is entirely heterochromatic, yet has wide-ranging effects on male fertility, fitness, and genome-wide gene expression. The genetic basis of this phenotypic variation is difficult to study, in part because we do not know the detailed organization of the Y chromosome. To study Y chromosome organization inD. melanogaster, we develop an assembly strategy involving thein silicoenrichment of heterochromatic long single-molecule reads and use these reads to create targetedde novoassemblies of heterochromatic sequences. We assigned contigs to the Y chromosome using Illumina reads to identify male-specific sequences. Our pipeline extends theD. melanogasterreference genome by 11.9-Mb, closes 43.8% of the gaps, and improves overall contiguity. The addition of 10.6 MB of Y-linked sequence permitted us to study the organization of repeats and genes along the Y chromosome. We detected a high rate of duplication to the pericentric regions of the Y chromosome from other regions in the genome. Most of these duplicated genes exist in multiple copies. We detail the evolutionary history of one sex-linked gene family—crystal-Stellate. While the Y chromosome does not undergo crossing over, we observed high gene conversion rates within and between members of thecrystal-Stellategene family,Su(Ste), andPCKR, compared to genome-wide estimates. Our results suggest that gene conversion and gene duplication play an important role in the evolution of Y-linked genes.
Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns
Authors: Kwasnieski Jamie C , Orr-Weaver Terry L , Bartel David P
Published: July 2018

Control of metazoan embryogenesis shifts from maternal to zygotic gene products as the zygotic genome becomes transcriptionally activated. In Drosophila, zygotic genome activation (ZGA) begins with a minor wave, but technical challenges have hampered the identification of early transcripts or obscured the onset of their transcription. Here, we develop an approach to isolate transcribed mRNAs and apply it over the course of the minor wave and the start of the major wave of Drosophila ZGA. Our results increase known genes of the minor wave by 10 fold and show that this wave is continuous and gradual. Transposable-element mRNAs are also produced, but discontinuously. Genes in the early and middle part of the minor wave are short with few if any introns, and their transcripts are frequently aborted and tend to have retained introns, suggesting that inefficient splicing as well as rapid cell divisions constrain the lengths of early transcripts.
Cancerous phenotypes associated with hypoxia-inducible factors are not influenced by the volatile anesthetic isoflurane in renal cell carcinoma
Authors: Sumi Chisato , Matsuo Yoshiyuki , Kusunoki Munenori , Shoji Tomohiro , Uba Takeo , Iwai Teppei , Bono Hidemasa , Hirota Kiichi
Published: July 2018

The possibility that anesthesia during cancer surgery may affect cancer recurrence, metastasis, and patient prognosis has become one of the most important topics of interest in cancer treatment. For example, the volatile anesthetic isoflurane was reported in several studies to induce hypoxia-inducible factors, and thereby enhance malignant phenotypesin vitro. Indeed, these transcription factors are considered critical regulators of cancer-related hallmarks, including “sustained proliferative signaling, evasion of growth suppressors, resistance to cell death, replicative immortality, angiogenesis, invasion, and metastasis.” This study aimed to investigate the impact of isoflurane on the growth and migration of derivatives of the renal cell line RCC4. We indicated that isoflurane treatment did not positively influence cancer cell phenotypes, and that hypoxia-inducible factors (HIFs) maintain hallmark cancer cell phenotypes including gene expressions signature, metabolism, cell proliferation and cell motility. The present results indicate that HIF activity is not influenced by the volatile anesthetic isoflurane.
Molecular typing and macrolide resistance analyses ofTreponema pallidumin heterosexuals and men who have sex with men communities in Japan, 2017
Authors: Kanai Mizue , Arima Yuzo , Nishiki Shingo , Shimuta Ken , Itoda Ichiro , Matsui Tamano , Oishi Kazunori , Ohnishi Makoto , Nakayama Shu-ichi
Published: July 2018

In recent years, syphilis notifications have increased dramatically in Japan. We performed molecular typing and analyzed macrolide resistance ofTreponema pallidumsamples collected from four clinics and a hospital in Tokyo and Osaka prefectures in 2017.

Macrolide resistant strain type 14d/f was found significantly more in heterosexual syphilis cases compared with those strains identified in men who have sex with men (MSM) syphilis cases. The proportion of 14d/f among heterosexuals was 79% (31/39) compared to 37% (7/19) among MSM [OR, 6.6 (95% CI, 1.7 to 26.7); P=0.002]. 83% (50/60) of the strains were identified as macrolide resistant with an A2058G mutation at the 23S rRNA gene. 90% (35/39) of the heterosexual strains were macrolide resistant, relative to 58% (11/19) of MSM strains; the odds of having the resistant mutation was considerably higher in heterosexuals compared with MSM [OR, 6.4 (95% CI, 1.3 to 33.5); P=0.02]. Heterosexual females and males showed similar distributions, and the results remained the same when restricted to men.

The strain type distribution and frequency of macrolide resistance differed substantially between heterosexual and MSM syphilis samples, suggesting distinct epidemiologic profiles for the two communities and insight into syphilis transmission dynamics in Japan.
Temporal Small RNA Expression Profiling Under Drought Reveals a Potential Regulatory Role of snoRNAs in Drought Responses of Maize
Authors: Zheng Jun , Zeng Erliang , Du Yicong , He Cheng , Hu Ying , Jiao Zhenzhen , Wang Kai , Li Wenxue , Ludens Maria , Fu Junjie , Wang Haiyan , White Frank F. , Wang Guoying , Liu Sanzhen
Published: July 2018

Small RNAs (sRNAs) are short noncoding RNAs that play roles in many biological processes, including drought responses in plants. However, how the expression of sRNAs dynamically changes with the gradual imposition of drought stress in plants is largely unknown. We generated time-series sRNA sequence data from maize seedlings under drought stress and under well-watered conditions at the same time points. Analyses of length, functional annotation, and abundance of 736,372 non-redundant sRNAs from both drought and well-watered data, as well as genome copy number and chromatin modifications at the corresponding genomic regions, revealed distinct patterns of abundance, genome organization, and chromatin modifications for different sRNA classes of sRNAs. The analysis identified 6,646 sRNAs whose regulation was altered in response to drought stress. Among drought-responsive sRNAs, 1,325 showed transient down-regulation by the seventh day, coinciding with visible symptoms of drought stress. The profiles revealed drought-responsive microRNAs, as well as other sRNAs that originated from ribosomal RNAs (rRNAs), splicing small nuclear RNAs, and small nucleolar RNAs (snoRNA). Expression profiles of their sRNA derivers indicated that snoRNAs might play a regulatory role through regulating stability of rRNAs and splicing small nuclear RNAs under drought condition.
Repeats Of Unusual Size in Plant Mitochondrial Genomes: Identification, Incidence and Evolution
Authors: Wynn Emily L. , Christensen Alan C.
Published: July 2018

Plant mitochondrial genomes have excessive size relative to coding capacity, a low mutation rate in genes and a high rearrangement rate. They also have non-tandem repeats in two size groups: a few large repeats which cause isomerization of the genome by recombination, and numerous repeats longer than 50bp, often found in exactly two copies per genome. It appears that repeats in the size range from several hundred to a few thousand base pair are underrepresented. The repeats are not well-conserved between species, and are infrequently annotated in mitochondrial sequence assemblies. Because they are much larger than expected by chance we call them Repeats Of Unusual Size (ROUS). The repeats consist of two functional classes, those that are involved in genome isomerization through frequent crossing over, and those for which crossovers are rare unless there are mutations in DNA repair genes, or the rate of double-strand breakage is increased. We systematically described and compared these repeats, which are important clues to mechanisms of DNA maintenance in mitochondria. We developed a tool to find non-tandem repeats and analyzed the complete mitochondrial sequences from 135 plant species. We observed an interesting difference between taxa: the repeats are larger and more frequent in the vascular plants. Analysis of closely related species also shows that plant mitochondrial genomes evolve in dramatic bursts of breakage and rejoining, complete with DNA sequence gain and loss, and the repeats are included in these events. We suggest an adaptive explanation for the existence of the repeats and their evolution.
High resolution discovery of chromatin interactions
Authors: Guo Yuchun , Krismer Konstantin , Closser Michael , Wichterle Hynek , Gifford David K.
Published: July 2018

Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) is a method for the genome-wide de novo discovery of chromatin interactions. Existing computational methods typically fail to detect weak or dynamic interactions because they use a peak-calling step that ignores paired-end linkage information. We have developed a novel computational method called Chromatin Interaction Discovery (CID) to overcome this limitation with an unbiased clustering approach for interaction discovery. CID outperforms existing chromatin interaction detection methods with improved sensitivity, replicate consistency, and concordance with other chromatin interaction datasets. In addition, CID also outperforms other methods in discovering chromatin interactions from HiChIP data. We expect that the CID method will be valuable in characterizing 3D chromatin interactions and in understanding the functional consequences of disease-associated distal genetic variations.
Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis inKlebsiella pneumoniae
Authors: Lam Margaret M. C. , Wyres Kelly L. , Judd Louise M. , Wick Ryan R. , Jenney Adam , Brisse Sylvain , Holt Kathryn E.
Published: July 2018

Background

Klebsiella pneumoniaeis a recognised agent of multidrug-resistant (MDR) healthcare-associated infections, however individual strains vary in their virulence potential due to the presence of mobile accessory genes. In particular, gene clusters encoding the biosynthesis of siderophores aerobactin (iuc) and salmochelin (iro) are associated with invasive disease and are common amongst hypervirulentK. pneumoniaeclones that cause severe community-associated infections such as liver abscess and pneumonia. Concerninglyiuchas also been reported in MDR strains in the hospital setting, where it was associated with increased mortality, highlighting the need to understand, detect and track the mobility of these virulence loci in theK. pneumoniaepopulation.

Methods

Here we examined the genetic diversity, distribution and mobilisation ofiucandiroloci among 2503K. pneumoniaegenomes using comparative genomics approaches, and developed tools for tracking them via genomic surveillance.

Results

Iroandiucwere detected at low prevalence (<10%). Considerable genetic diversity was observed, resolving into fiveiroand sixiuclineages that show distinct patterns of mobilisation and dissemination in theK. pneumoniaepopulation. The major burden ofiucandiroamongst the genomes analysed was due to two linked lineages (iuc1/iro1, 74% andiuc2/iro2, 14%), each carried by a distinct non-self-transmissible IncFIBKvirulence plasmid type that we designate KpVP-1 and KpVP-2. These dominant types also carry hypermucoidy (rmpA) determinants and include all previously described virulence plasmids ofK. pneumoniae. The otheriucandirolineages were associated with diverse plasmids, including some carrying FII conjugative transfer regions and some imported fromE. coli; the exceptions wereiro3(mobilised byICEKp1), andiuc4(fixed in the chromosome ofK. pneumoniaesubspeciesrhinoscleromatis).Iro/iucMGEs appear to be stably maintained at high frequency within known hypervirulent strains (ST23, ST86, etc), but were also detected at low prevalence in others such as MDR strain ST258.

Conclusions

Iucandiroare mobilised inK. pneumoniaevia a limited number of MGEs. This study provides a framework for identifying and tracking these important virulence loci, which will be important for genomic surveillance efforts including monitoring for the emergence of hypervirulent MDRK. pneumoniaestrains.
Comparative genomics-first approach to understand diversification of secondary metabolite biosynthetic pathways in symbiotic dinoflagellates
Authors: Beedessee Girish , Hisata Kanako , Roy Michael C. , Van Dolah Frances M. , Satoh Noriyuki , Shoguchi Eiichi
Published: July 2018

Symbiotic dinoflagellates of the genus Symbiodinium are photosynthetic and unicellular. They possess smaller nuclear genomes than other dinoflagellates and produce structurally specialized, biologically active, secondary metabolites. Polyketide biosynthetic genes of toxic dinoflagellates have been studied extensively using transcriptomic analyses; however, a comparative genomic approach to understand secondary metabolism has been hampered by their large genome sizes. Here, we use a combined genomic and metabolomics approach to investigate the structure and diversification of secondary metabolite genes to understand how chemical diversity arises in three decoded Symbiodinium genomes (A3, B1 and C). Our analyses identify 71 polyketide synthase and 41 non-ribosomal peptide synthetase genes from two newly decoded genomes of clades A3 and C. Additionally, phylogenetic analyses indicate that almost all of the gene families are derived from lineage-specific gene duplications in Symbiodinium clades, suggesting divergence for environmental adaptation. Few metabolic pathways are conserved among the three clades and we detect metabolic similarity only in the recently diverged clades, B1 and C. We establish that secondary metabolism protein architecture guides substrate specificity and that gene duplication and domain shuffling have resulted in diversification of secondary metabolism genes.
Does the interaction between partnership status and average progesterone level predict women’s preferences for facial masculinity?
Authors: DeBruine Lisa M , Hahn Amanda C , Jones Benedict C
Published: July 2018

Many studies have attempted to identify biological factors that reliably predict individual differences in women’s preferences for masculine male faces. Marcinkowska et al. (2018, Hormones & Behavior) recently reported that women’s (N=102) preferences for facial masculinity were predicted by the interaction between their relationship status (partnered versus unpartnered) and average progesterone level. Because previous findings for between-women differences in masculinity preferences have often not replicated well, we attempted to replicate Marcinkowska et al’s result in an open data set from another recent study that had not tested this hypothesis (Jones et al., 2018 Psychological Science). In this sample of 316 women, we found that facial masculinity preferences were predicted by the interaction between women’s relationship status and average progesterone level, consistent with Marcinkowska et al’s results. Together, these findings suggest that the combined effects of relationship status and average progesterone level may predict facial masculinity preferences relatively reliably.
An unbiased template of theDrosophilabrain and ventral nerve cord
Authors: Bogovic John A , Otsuna Hideo , Heinrich Larissa , Ito Masayoshi , Jeter Jennifer , Meissner Geoffrey , Nern Aljoscha , Colonell Jennifer , Malkesman Oz , Ito Kei , Saalfeld Stephan
Published: July 2018

The fruit flyDrosophila melanogasteris an important model organism for neuroscience with a wide array of genetic tools that enable the mapping of individuals neurons and neural subtypes. Brain templates are essential for comparative biological studies because they enable analyzing many individuals in a common reference space. Several central brain templates exist forDrosophila, but every one is either biased, uses sub-optimal tissue preparation, is imaged at low resolution, or does not account for artifacts. No publicly availableDrosophilaventral nerve cord template currently exists. In this work, we created high-resolution templates of theDrosophilabrain and ventral nerve cord using the best-available technologies for imaging, artifact correction, stitching, and template construction using groupwise registration. We evaluated our central brain template against the four most competitive, publicly available brain templates and demonstrate that ours enables more accurate registration with fewer local deformations in shorter time.
The application of Hadoop in Structural Bioinformatics
Authors: Alnasir Jamie , Shanahan Hugh P.
Published: July 2018

The paper reviews the use of the Hadoop platform in Structural Bioinformatics applications. Specifically, we review a number of implementations using Hadoop of high-throughput analyses, e.g. ligand-protein docking and structural alignment, and their scalability in comparison with other batch schedulers and MPI. We find that these deployments for the most part use known executables called from MapReduce rather than rewriting the algorithms. The scalability exhibits a variable behaviour in comparison with other batch schedulers, particularly as direct comparisons on the same platform are generally not available. We do note there is some evidence that MPI implementations scale better than Hadoop. A significant barrier to the use of the Hadoop ecosystem is the difficulty of the interface and configuration of a resource to use Hadoop. This will improve over time as interfaces to Hadoop e.g. Spark improve, usage of cloud platforms (e.g. Azure and AWS) increases and approaches such as the Workflow Definition Language are taken up.
Joint Speed Discrimination and Augmentation For Prosthesis Feedback
Authors: Earley Eric J. , Johnson Reva E. , Hargrove Levi J. , Sensinger Jon W.
Published: July 2018

Sensory feedback is critical in fine motor control, learning, and adaptation. However, robotic prosthetic limbs currently lack the feedback segment of the communication loop between user and device. Artificial sensory feedback can close this gap, but sometimes this improvement only persists when users cannot see their prosthesis. suggesting the provided feedback is redundant with vision. Thus, given the choice, users rely on vision over artificial feedback. To effectively augment vision, sensory feedback must provide information that vision cannot provide or provides poorly. Although vision is known to be less precise at estimating speed than position, no work has compared speed precision of biomimetic arm movements. In this study, we investigated the uncertainty of visual speed estimates as defined by different virtual arm movements. We found that uncertainty was greatest for visual estimates of joint speeds, compared to absolute or linear endpoint speeds. Furthermore, this uncertainty increased when the joint reference frame speed varied over time, potentially caused by an overestimation of joint speed. Finally, we demonstrate a joint-based sensory feedback paradigm capable of significantly reducing joint speed uncertainty when paired with vision. Ultimately, this work may lead to improved prosthesis control and capacity for motor learning.
3D-printable tools for developmental biology: Improving embryo injection and screening techniques through 3D-printing technology
Authors: Truchado-Garcia Marta , Harland Richard M. , Abrams Michael J.
Published: July 2018

Developmental biology requires rapid embryo injections and screening. We applied new affordable high-resolution 3D-printing to createfiveeasily modifiable stamp-mold tools that greatly increase injection and screening speed, while simultaneously reducing the harmful aspects of these processes. We designed two stamps that use different approaches to improve the injection efficiency for two different types of embryo, first for embryos from the snailCrepidula fornicata, and second, for those from the spiderParasteatoda tepidariorum. Both drastically improved injection speeds and embryo survival rates, even in novice hands. The other three tools were designed for rapid side-by-side organism orientating and comparison. The first screening tool allows for optimal imaging inXenopus laevistadpoles, while the second and third facilitate rapid high-throughput screening ofXenopus tropicalistadpoles andDanio reriojuveniles, respectively. These designs can act as templates for many injection or screening applications.
Extreme genetic structure and dynamic range evolution in a montane passerine bird: implications for tropical diversification
Authors: Cadena Carlos Daniel , Pérez-Emán Jorge L. , Cuervo Andrés M. , Céspedes Laura N. , Epperly Kevin L. , Klicka John T.
Published: July 2018

Aim

Employ phylogeographic analyses of a widespread species complex to examine the role of historical and evolutionary processes in the origin and maintenance of high species diversity in the Neotropical montane region.

Location

Neotropical highlands.

Taxon

Henicorhinawood-wrens (Aves, Troglodytidae).

Methods

We collected mtDNA sequence data for 288 individuals thoroughly covering the range of theHenicorhina leucophryscomplex from Mexico to Bolivia. Sequences were employed to characterize population structure, infer phylogenetic relationships among populations and their divergence times, examine lineage accumulation through time, and identify presumptive species using coalescent methods. We also explored the origin of elevational and latitudinal replacements involved in spatial changes in species assemblages in the Andes.

Results

We found remarkable genetic structure within the complex, which consists of numerous lineages reaching >12% sequence divergence; most divergent populations occur in areas separated by topographic barriers but several of them, typically not sister to each other, co-occur with elevational segregation on mountain slopes or replace each other with latitude along the Andes. Some close relatives occur in areas separated by thousands of kilometers, with more distant relatives occupying intervening areas. The complex likely originated in the Mexican highlands and expanded extensively in South America while diverging rapidly at a constant rate into many different lineages which have persisted for millions of years. Coalescent analyses consistently revealed that the complex may comprise more than 30 species; while we do not suggest these presumptive species should be recognized by taxonomists in the absence of additional data,H. leucophrysis a distant outlier among New World birds in terms of high lineage diversity within a single recognized species.

Main Conclusions

Our study captured wood-wren lineages in the act of building up diversity via divergence and persistence in allopatry, achievement of secondary sympatry, and coexistence at the landscape scale mediated by ecological and evolutionary divergence. Although dispersal by wood-wrens is restricted at present and this likely accounts for strong population structure across topographic barriers, their ranges have been dynamic, managing to disperse over much of the montane Neotropics. Phases of expansion and contraction of ranges and localized extinctions of populations likely account for phylogeographic patterns which are precursors to the origin of new species and the accumulation of diversity in tropical mountains.
Microscale light management and inherent optical properties of intact corals studied with optical coherence tomography
Authors: Wangpraseurt Daniel , Jacques Steven , Lyndby Niclas , Holm Jacob Boiesen , Pages Christine Ferrier , Kühl Michael
Published: July 2018

Coral reefs are highly productive photosynthetic systems and coral optics studies suggest that such high efficiency is due to optimised light scattering by coral tissue and skeleton. Here, we characterise the inherent optical properties, i.e., the scattering coefficient, μs, and the anisotropy of scattering, g, of 8 intact coral species using optical coherence tomography (OCT). Specifically, we describe light scattering by coral skeletons, coenoarc tissues, polyp tentacles and areas covered by fluorescent pigments (FP). Our results reveal that light scattering between coral species ranges from μs = 3 mm−1 (Stylophora pistillata) to μs= 25 mm−1 (Echinopora lamelosa). For Platygyra pini, μs was 10-fold higher for tissue vs skeleton, while in other corals (e.g. Hydnophora pilosa) no difference was found between tissue and skeletal scattering. Tissue scattering was 3-fold enhanced in coenosarc tissues (μs = 24.6 mm−1) vs polyp tentacles (μs = 8.3 mm−1) in Turbinaria reniformis. FP scattering was almost isotropic when FP were organized in granule chromatophores (g=0.34) but was forward directed when FP were distributed diffusely in the tissue (g=0.96). Our study provides detailed measurements of coral scattering and establishes a rapid approach for characterising optical properties of photosynthetic soft tissues via OCT in vivo.
A subfunctionalization epistasis model to evaluate homeologous gene interactions in allopolyploid wheat
Authors: Santantonio Nicholas , Jannink Jean-Luc , Sorrells Mark E.
Published: July 2018

1

Hybridization between related species results in the formation of an allopolyploid with multiple subgenomes. These subgenomes will each contain complete, yet evolutionarily divergent, sets of genes. Like a diploid hybrid, allopolyploids will have two versions, or homeoalleles, for every gene. Partial functional redundancy between homeologous genes should result in a deviation from additivity. These epistatic interactions between homeoalleles are analogous to dominance effects, but are fixed across subgenomes through self pollination. An allopolyploid can be viewed as an immortalized hybrid, with the opportunity to select and fix favorable homeoallelic interactions within inbred varieties. We present a subfunctionalization epistasis model to estimate the degree of functional redundancy between homeoallelic loci and a statistical framework to determine their importance within a population. We provide an example using the homeologous dwarfing genes of allohexaploid wheat,Rht-1, and search for genome-wide patterns indicative of homeoallelic subfunctionalization in a breeding population. Using the IWGSC RefSeq vl.0 sequence, 23,796 homeoallelic gene sets were identified and anchored to the nearest DNA marker to form 10,172 homeologous marker sets. Interaction predictors constructed from products of marker scores were used to fit the homeologous main and interaction effects, as well as estimate whole genome genetic values. Some traits displayed a pattern indicative of homeoallelic subfunctionalization, while other traits showed a less clear pattern or were not affected. Using genomic prediction accuracy to evaluate importance of marker interactions, we show that homeologous interactions explain a portion of the non-additive genetic signal, but are less important than other epistatic interactions.
Probabilities of tree topologies with temporal constraints and diversification shifts
Authors: Didier Gilles
Published: July 2018

Dating the tree of life is a task far more complicated that only determining the evolutionary relationships between species. It is therefore of interest to develop approaches able to deal with undated phylogenetic trees.

The main result of this work is a method to compute probabilities of undated phylogenetic trees under piecewiseconstant-birth-death-sampling models by constraining some of the divergence times to belong to given time intervals and by allowing diversification shifts on certain clades. The computation is quite fast since its time complexity is quadratic with the size of the tree topology and linear with the number of time constraints and of “pieces” in the model.

The interest of this computation method is illustrated with three applications, namely,

to compute the exact distribution of the divergence times of a tree topology with temporal constraints,

to directly sample the divergence times of a tree topology, and

to test for a diversification shift at a given clade.
Targeting a Therapy-Resistant Cancer Cell State Using Masked Electrophiles as GPX4 Inhibitors
Authors: Eaton John K. , Furst Laura , Ruberto Richard A. , Moosmayer Dieter , Hillig Roman C. , Hilpmann André , Zimmermann Katja , Ryan Matthew J. , Niehues Michael , Badock Volker , Kramm Anneke , Chen Sixun , Clemons Paul A. , Gradl Stefan , Montagnon Claire , Lazarski Kiel E. , Christian Sven , Bajrami Besnik , Neuhaus Roland , Eheim Ashley L. , Viswanathan Vasanthi S. , Schreiber Stuart L.
Published: July 2018

We recently discovered that inhibition of the lipid peroxidase GPX4 can selectively kill cancer cells in a therapy-resistant state through induction of ferroptosis. Although GPX4 lacks a conventional druggable pocket, covalent small-molecule inhibitors are able to overcome this challenge by reacting with the GPX4 catalytic selenocysteine residue to eliminate enzymatic activity. Unfortunately, all currently-reported GPX4 inhibitors achieve their activity through reactive chloroacetamide groups. We demonstrate that such chloroacetamide-containing compounds are poor starting points for further advancement given their promiscuity, instability, and low bioavailability. Development of improved GPX4 inhibitors, including those with therapeutic potential, requires the identification of new electrophilic chemotypes and mechanisms of action that do not suffer these shortcomings. Here, we report our discovery that nitrile oxide electrophiles, and a set of remarkable chemical transformations that generates them in cells from masked precursors, provide an effective strategy for selective targeting of GPX4. Our results, which include structural insights, target engagement assays, and diverse GPX4-inhibitor tool compounds, provide critical insights that may galvanize development of improved compounds that illuminate the basic biology of GPX4 and therapeutic potential of ferroptosis induction. In addition, our discovery that nitrile oxide electrophiles engage in highly selective cellular interactions and are bioavailable in their masked forms may be relevant for targeting other currently undruggable proteins, such as those revealed by recent proteome-wide ligandability studies.
Yeast Chd1p remodels nucleosomes with unique DNA unwrapping and translocation dynamics
Authors: Kirk Jaewon , Lee Ju Yeon , Lee Yejin , Kang Chanshin , Shin Soochul , Lee Eunhye , Song Ji-Joon , Hohng Sungchul
Published: July 2018

Chromodomain-helicase-DNA-binding protein 1 (CHD1) remodels chromatin by translocating nucleosomes along DNA, but its mechanism remains poorly understood. Here, we employ a single-molecule fluorescence approach to characterize nucleosome remodeling by yeast CHD1 (Chd1p). We show that Chd1p translocates nucleosomes in steps of multiple base pairs per ATP. ATP binding to Chd1p induces a transient unwrapping of the exit-side DNA, and facilitates nucleosome translocation. ATP hydrolysis induces nucleosome translocation, which is followed by the rewrapping upon the release of the hydrolyzed nucleotide. Multiple Chd1ps binding to a single nucleosome sequentially moves a histone octamer with a preference to the center of DNA fragments, suggesting a new mechanism for regularly spaced nucleosome generation by Chd1p. Our results reveal the unique mechanism by which Chd1p remodels nucleosomes.

Significance Statement

There are four major ATP-dependent chromatin remodeler families: SWI/SNF, ISWI, CHD, and INO80/SWR1. The remodeling mechanisms of SWI/SNF and ISWI chromatin remodelers have been elucidated through extensive single-molecule studies, but it remains poorly understood how CHD chromatin remodeler operate. We use single-molecule FRET techniques, and show that Yeast CHD1 uses unique mechanisms to remodel a nucleosome.