bluuebunny/crossref_metadata_2025 huggingface dataset:
Re-description of two contemporaneous mesorostrine teleosauroids (Crocodylomorpha: Thalattosuchia) from the Bathonian of England and insights into the early evolution of Machimosaurini
Authors: Johnson Michela M , Young Mark T , Brusatte Stephen L
Published: April 2019

Teleosauroidea was a clade of successful, morphologically diverse, ancient crocodylomorphs that were integral in coastal marine/lagoonal environments during the Jurassic. Within Teleosauroidea, the macrophagous/durophagous tribe Machimosaurini evolved specialized feeding strategies (e.g. hypertrophied jaw musculature and blunt, heavily ornamented dentition) and large body sizes (> 7 m), becoming an important component of Middle and Late Jurassic ecosystems. These ocean-dwelling giants are well known from the Callovian (Lemmysuchus) of Europe and the UK, and from the Kimmeridgian–Tithonian (Machimosaurus) of Europe and northern Africa. There are reports of fragmentary machimosaurin material from the Bathonian of Africa, but the overall Bathonian teleosauroid material is poorly understood. While multiple specimens were described during the 19th and 20th centuries, little research has been done since. Here we re-describe two historically important Bathonian species from near Oxford, UK. We demonstrate that both ‘Steneosaurus’ larteti and ‘Steneosaurus’ boutilieri are valid taxa and we establish neotypes for both species and two new genera, Deslongchampsina and Yvridiosuchus. Our cladistic analysis finds Yvridiosuchus boutilieri as a basal member of Machimosaurini and Deslongchampsina lartetito be closely related to Steneosaurus heberti. Interestingly, four distinct teleosauroid ecomorphotypes are present in the Bathonian of Europe and teleosauroid ecomorphological diversity continued throughout the Callovian and Kimmeridgian/Tithonian in Europe and England.
A Bipartite Begomovirus Infecting Boerhavia erecta (Family Nyctaginaceae) in the Dominican Republic Represents a Distinct Phylogenetic Lineage and has a High Degree of Host Specificity
Authors: Melgarejo Tomas A. , Rojas Maria R. , Gilbertson Robert L.
Published: April 2019

Boerhavia erecta plants in and around agricultural fields in the Azua Valley of the southeastern Dominican Republic often show striking golden mosaic symptoms. Leaf samples from B. erecta plants showing these symptoms were collected in 2012 and 2013, and PCR tests with degenerate primers revealed begomovirus DNA-A and DNA-B components. The complete sequences of the DNA-A and DNA-B components of four isolates show a high degree of sequence identity (>96%) and a genome organization typical of New World (NW) bipartite begomoviruses. Sequence comparisons and phylogenetic analyses revealed that these isolates composed a new phylogenetic lineage of NW bipartite begomoviruses. The most closely related begomovirus is Merremia mosaic virus, a weed-infecting species from Puerto Rico. Because DNA-A sequence identities are well below the 91% threshold, these isolates represent a new begomovirus species, for which the name Boerhavia golden mosaic virus (BoGMV) is proposed. Infectious cloned BoGMV DNA-A and DNA-B components induced golden mosaic symptoms in agroinoculated B. erecta plants, thereby fulfilling Koch’s postulates for this disease. Agroinoculation and mechanical transmission experiments revealed that BoGMV has an unusually narrow host range, limited to members of the family Nyctaginaceae and not including the permissive host Nicotiana benthamiana. The inability of BoGMV to infect N. benthamiana was due to a deficiency in cell-to-cell movement but not to a unique amino acid residue in the movement protein.
Signal complexity communicates aggressive intent during contests, but the process is disrupted by noise
Authors: Kareklas Kyriacos , Wilson James , Kunc Hansjoerg P. , Arnott Gareth
Published: April 2019

Contestants use displays to signal their aggressive intent and settle disputes before they escalate. For birds, this is often in the form of song, which can vary in structural complexity. The role of song complexity in signalling aggressive intent has not been fully established, and its efficacy could be influenced by background noise levels. Using playback experiments, we found that in European robins,
Erithacus rubecula,
song complexity signalled sender aggression and affected receiver response. However, increased noise impacted the ability of contestants to adjust response based on opponent song complexity. These findings provide new evidence regarding the use of acoustic signal complexity for assessing opponent aggression and that noise can influence contest behaviour by interrupting this process, which could impose fitness consequences.
General rogue wave solutions of the coupled Fokas–Lenells equations and non-recursive Darboux transformation
Authors: Ye Yanlin , Zhou Yi , Chen Shihua , Baronio Fabio , Grelu Philippe
Published: April 2019

We formulate a non-recursive Darboux transformation technique to obtain the general
n
th-order rational rogue wave solutions to the coupled Fokas–Lenells system, which is an integrable extension of the noted Manakov system, by considering both the double-root and triple-root situations of the spectral characteristic equation. Based on the explicit fundamental and second-order rogue wave solutions, we demonstrate several interesting rogue wave dynamics, among which are coexisting rogue waves and anomalous Peregrine solitons. Our solutions are generalized to include the complete background-field parameters and therefore helpful for future experimental study.
Kinetics of steel slag dissolution: from experiments to modelling
Authors: Ragipani Raghavendra , Bhattacharya Sankar , Suresh Akkihebbal K.
Published: April 2019

Carbon dioxide sequestration via carbonation of steel slags is a promising way of combining two waste products to create value. Understanding the dissolution kinetics of steel slags, which are alkaline and rich in calcium, in acidic media is essential to configure such a process. In this study, we seek to analyse the dissolution mechanism from experimental studies and develop a mathematical model considering the heterogeneous characteristics of slag. We found that the reduction in calcium extraction efficiency with an increase in particle size, which is normally associated with surface passivation or non-uniformity of samples, can be explained by considering the morphological features associated with the distribution of MgO–FeO (RO) phase in the calcium silicate matrix. We present a population balance model and show that the reduction in calcium extraction efficiency in coarse particle fractions is due to increased
sporulation
of the RO phase. The findings in the study suggest that the leaching of metal ions from slag is controlled by proton-promoted surface dissolution reaction, where the dependence of acid concentration follows the Langmuir–Hinshelwood adsorption isotherm. The model shows good agreement with a large set of parametric studies and demonstrates the importance of considering morphological features, as we progress towards development of
a priori
dissolution models for multi-mineral oxides and silicates.
On the role of localizations in buckling of axially compressed cylinders
Authors: Groh R. M. J. , Pirrera A.
Published: April 2019

The collapse of axially compressed cylinders by buckling instability is a classic problem in engineering mechanics. We revisit the problem by considering fully localized post-buckling states in the form of one or multiple dimples. Using nonlinear finite-element methods and numerical continuation algorithms, we trace the evolution of odd and even dimples into one axially localized ring of circumferentially periodic diamond-shaped waves. The growth of the post-buckling pattern with varying compression is driven by homoclinic snaking with even- and odd-dimple solutions intertwined. When the axially localized ring of diamond-shaped buckles destabilizes, additional circumferential snaking sequences ensue that lead to the Yoshimura buckling pattern. The unstable single-dimple state is a mountain-pass point in the energy landscape and therefore forms the smallest energy barrier between the pre-buckling and post-buckling regimes. The small energy barrier associated with the mountain-pass point means that the compressed, pre-buckled cylinder is exceedingly sensitive to perturbations once the mountain-pass point exists. We parameterize the compressive onset of the single-dimple mountain-pass point with a single non-dimensional parameter, and compare the lower-bound buckling load suggested by this parameter with over 100 experimental data points from the literature. Good correlation suggests that the derived knockdown factor provides a less conservative design load than NASA's SP-8007 guideline.
Avian functional responses to landscape recovery
Authors: Ikin Karen , Barton Philip S. , Blanchard Wade , Crane Mason , Stein John , Lindenmayer David B.
Published: April 2019

Restoring native vegetation in agricultural landscapes can reverse biodiversity declines via species gains. Depending on whether the traits of colonizers are complementary or redundant to the assemblage, species gains can increase the efficiency or stability of ecological functions, yet detecting these processes is not straightforward. We propose a new conceptual model to identify potential changes to complementarity and redundancy in response to landscape change via relative changes in taxonomic and functional richness. We applied our model to a 14-year study of birds across an extensive agricultural region. We found compelling evidence that high levels of landscape-scale tree cover and patch-scale restoration were significant determinants of functional change in the overall bird assemblage. This was true for every one of the six traits investigated individually, indicating increased trait-specific functional complementarity and redundancy in the assemblage. Applying our conceptual model to species diversity data provided new insights into how the return of vertebrates to restored landscapes may affect ecological function.
Haemolymph removal by
Varroa
mite destabilizes the dynamical interaction between immune effectors and virus in bees, as predicted by Volterra's model
Authors: Annoscia Desiderato , Brown Sam P. , Di Prisco Gennaro , De Paoli Emanuele , Del Fabbro Simone , Frizzera Davide , Zanni Virginia , Galbraith David A. , Caprio Emilio , Grozinger Christina M. , Pennacchio Francesco , Nazzi Francesco
Published: April 2019

The association between the deformed wing virus and the parasitic mite
Varroa destructor
has been identified as a major cause of worldwide honeybee colony losses. The mite acts as a vector of the viral pathogen and can trigger its replication in infected bees. However, the mechanistic details underlying this tripartite interaction are still poorly defined, and, particularly, the causes of viral proliferation in mite-infested bees. Here, we develop and test a novel hypothesis that mite feeding destabilizes viral immune control through the removal of both virus and immune effectors, triggering uncontrolled viral replication. Our hypothesis is grounded on the predator–prey theory developed by Volterra, which predicts prey proliferation when both predators and preys are constantly removed from the system. Consistent with this hypothesis, we show that the experimental removal of increasing volumes of haemolymph from individual bees results in increasing viral densities. By contrast, we do not find consistent support for alternative proposed mechanisms of viral expansion via mite immune suppression or within-host viral evolution. Our results suggest that haemolymph removal plays an important role in the enhanced pathogen virulence observed in the presence of feeding
Varroa
mites. Overall, these results provide a new model for the mechanisms driving pathogen–parasite interactions in bees, which ultimately underpin honeybee health decline and colony losses.
The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation
Authors: Batki Julia , Schnabl Jakob , Wang Juncheng , Handler Dominik , Andreev Veselin I. , Stieger Christian E. , Novatchkova Maria , Lampersberger Lisa , Kauneckaite Kotryna , Xie Wei , Mechtler Karl , Patel Dinshaw J. , Brennecke Julius
Published: April 2019

The PIWI-interacting RNA (piRNA) pathway protects animal genome integrity in part through establishing repressive heterochromatin at transposon loci. Silencing requires piRNA-guided targeting of nuclear PIWI proteins to nascent transposon transcripts, yet the subsequent molecular events are not understood. Here, we identify SFiNX (Silencing Factor interacting Nuclear eXport variant), an interdependent protein complex required for Piwi-mediated co-transcriptional silencing in Drosophila. SFiNX consists of Nxf2-Nxt1, a gonad-specific variant of the heterodimeric mRNA export receptor Nxf1-Nxt1, and the Piwi-associated protein Panoramix. SFiNX mutant flies are sterile and exhibit transposon de-repression because piRNA-loaded Piwi is unable to establish heterochromatin. Within SFiNX, Panoramix recruits the heterochromatin effectors, while the RNA binding Nxf2 protein licenses co-transcriptional silencing. Our data reveal how Nxf2 evolved from an RNA transport receptor into a co-transcriptional silencing factor. Thus, NXF-variants, which are abundant in metazoans, can have diverse molecular functions and might have been co-opted for host genome defense more broadly.
Gene regulatory network inference and analysis of multidrug-resistant Pseudomonas aeruginosa
Authors: Filho Fernando Medeiros , do Nascimento Ana Paula Barbosa , dos Santos Marcelo Trindade , Carvalho-Assef Ana Paula D’Alincourt , da Silva Fabricio Alves Barbosa
Published: April 2019

Background

Healthcare-associated infections caused by bacteria such as Pseudomonas aeruginosa are a major public health problem worldwide. Gene regulatory networks computationally represent interactions among regulatory genes and their targets, an important approach to understand bacterial behavior and to provide novel ways of overcoming scientific challenges, including the identification of potential therapeutic targets and the development of new drugs.

Objectives

Our goal in this manuscript is to present a reconstruction of multidrug-resistant P. aeruginosa gene regulatory network and to analyze its topological properties.

Methods

The methodology was based on gene orthology inference by the reciprocal best hit method. We used the genome of P. aeruginosa CCBH4851 as the basis of the reconstruction process. This multidrug-resistant strain is representative of an endemic outbreak in Brazilian territory belonging to ST277.

Findings

As the main finding, we obtained a network with a larger number of regulatory genes, target genes and interactions compared to previous work. Topological analysis results are accordant to the complex network representation of biological processes.

Main conclusions

The network properties are consistent with P. aeruginosa biological features. To the best of our knowledge, the P. aeruginosa gene regulatory network presented here is the most complete version available to date.
Detection and characterization of a novel copper-dependent intermediate in a lytic polysaccharide monooxygenase
Authors: Singh Raushan K. , Oort Bart v. , Möllers Benedikt , Russo David A. , Singh Ranjitha , Weihe Høgni , Tiwari Manish K. , Croce Roberta , Jensen Paul E. , Felby Claus , Bjerrum Morten J.
Published: April 2019

Lytic polysaccharide monooxygenases (LPMOs) are copper-containing enzymes capable of oxidizing crystalline cellulose and the enzyme has large practical application in the process of refining biomass. The LPMO catalytic mechanism still remains debated despite several proposed reaction mechanisms. Here, we report a long-lived intermediate (t½= 6 – 8 minutes) observed in an LPMO fromThermoascus aurantiacus(TaLPMO9A). The intermediate with a strong absorption around 420 nm is formed when reduced LPMO-Cu(I) reacts with H2O2. UV-vis absorption spectroscopy, electron paramagnetic resonance (EPR), and stopped-flow spectroscopy indicate that the observed long-lived intermediate involves the copper center and a nearby tyrosine (Tyr175). We propose that the reaction with H2O2first forms a highly reactive short-lived Cu(III)-intermediate which is subsequently transformed into the observed long-lived copper-dependent intermediate. Since sub-equimolar amount of H2O2to LPMO boosts oxidation of phosphoric acid swollen cellulose (PASC) suggests that the long-lived copper-dependent intermediate is part of the catalytic mechanism for LPMOs. The proposed mechanism offers new perspectives in the oxidative reaction mechanism of copper enzymes and hence for the biomass oxidation and the reactivity of copper in biological systems.
Incidence, predictors and reasons for initial regimen modifications in patients on antiretroviral therapy in Witbank, South Africa, 2003-2017
Authors: Bapela Moshibudi Poncho , Kuonza Lazarus Rugare , Musekiwa Alfred , Summers Robert
Published: April 2019

Background

Antiretroviral therapy (ART) is associated with unpleasant adverse effects that may require modification of regimens. ART modifications may lead to poor treatment outcomes. We determined the incidence, reasons and predictors for modification of initial ART regimens.

Methods

We retrospectively analysed data from Witbank pharmacovigilance sentinel site, South Africa. Censoring targeted the first incident of ART modification from the initial regimen. We included human immunodeficiency virus (HIV)-infected patients on ART, aged more than 18 years. We used the Cox-proportional hazard model to identify predictors for changing initial ART regimens.

Results

Among 2, 045 eligible patients, 38% (n=783) had their initial ART regimens changed. The overall incidence rate of ART modification was 10.0 per 100 person-years within a follow-up period of 7 794.6 person-years (PYs). Reasons for changing were adverse drug reactions (ADRs) (60%), prescriber’s decisions (37%), drug toxicity (26%) and treatment failure (12%). The most commonly changed regimens were stavudine (68%) and zidovudine (44%) based regimens. Stavudine-based regimen had the highest changing rate of 13.6 per 100 PYs compared to zidovudine (8.0 per 100 PYs) and tenofovir (6.5 per 100 PYs). Using tenofovir as reference, stavudine (aHR 2.3; 95% CI 1.8-2.9; p<0.001) and zidovudine (aHR 1.5; 95% CI 1.2-3.2; p<0.001) based regimens were significantly associated with regimen modifications. The predictors for changing ART regimens included drug toxicity (aHR 2.6; 95% CI 2.1-3.1), ADRs (aHR 2.1; 95% CI 1.3-3.2), treatment failure (aHR 2.0; 95% CI 1.5-2.4), baseline cd4 count of ≥200 (aHR 1.7; 95% CI 1.3-2.1) and initiation regimens (stavudine and zidovudine).

Conclusion

The findings were suggestive of a moderate incidence of initial ART regimen changing. Patients on stavudine and zidovudine based regimens changed primarily due to ADRs and drug toxicity. We recommended that clinicians should consider changing patients who are still on stavudine-containing regimens, however, changing should be individualized.
Identifying and validating housekeeping hybridPrunussp. genes for root gene-expression studies
Authors: Bastías Adriana , Oviedo Kristen , Almada Rubén , Correa Francisco , Sagredo Boris
Published: April 2019

Prunus rootstock belonging to subgeneraAmygdalus(peach),Prunus(plum) andCerasus(cherry) are either from the same species as the scion or another one. The number of inter-species (including inter-subgenera) hybrids have increased as a result of efforts to broaden the genetic basis for biotic and abiotic resistance/tolerance. Identifying genes associated with important traits and responses requires expression analysis. Relative quantification is the simplest and most popular alternative, which requires reference genes (housekeeping) to normalize RT-qPCR data. However, there is a scarcity of validated housekeeping genes for hybrid Prunus rootstock species. This research aims to increase the number of housekeeping genes suitable for Prunus rootstock expression analysis.

Twenty-one candidate housekeeping genes were pre-selected from previous RNAseq data that compared the response of root transcriptomes of two rootstocks subgenera to hypoxia treatment, ‘Mariana 2624’ (P. cerasiferaEhrh.×P. munsonianaW. Wight & Hedrick), and ‘Mazzard F12/1’ (P. aviumL.). Representing groups of low, intermediate or high levels of expression, the genes were assayed by RT-qPCR at 72 hours of hypoxia treatment and analyzed with NormFinder software. A sub-set of seven housekeeping genes that presented the highest level of stability were selected, two with low levels of expression (Unknown 3, Unknown 7) and five with medium levels (GTB 1, TUA 3, ATPase P, PRT 6, RP II). The stability of these genes was evaluated under different stress conditions, cold and heat with the hybrid ‘Mariana 2624’ and N nutrition with the hybrids ‘Colt’ (P. avium×P. pseudocerasusLindl.) and ‘Garnem’ [P. dulcisMill.× (P. persicaL.×P. davidianaCarr.)]. The algorithms of geNorm and BestKeeper software also were used to analyze the performance of these genes as housekeepers.

Stability rankings varied according to treatments, genotypes and the software for evaluation, but the geneGBT 1often had the highest ranking. However, most of the genes are suitable depending on the stressor and/or genotype to be evaluated. No optimal number of reference genes could be determined with geNorm software when all conditions and genotypes were considered. These results strongly suggest that relative RT-qPCR should be analyzed separately with their respective best housekeeper according to the treatment and/or genotypes inPrunusspp rootstocks.
Muropeptides Stimulate Growth Resumption from Stationary Phase inEscherichia coli
Authors: Jõers Arvi , Vind Kristiina , Hernández Sara B. , Maruste Regina , Pereira Marta , Brauer Age , Remm Maido , Cava Felipe , Tenson Tanel
Published: April 2019

When nutrients run out, bacteria enter a dormant metabolic state. This low or undetectable metabolic activity helps bacteria to preserve their scant reserves for future, but also diminishes their ability to trace the environment for new growth-promoting substrates. However, neighboring microbial growth is a sure indicator of favorable environment and thus, can serve as a cue for exiting the dormancy. Here we report that forEscherichia colithis cue is the basic peptidoglycan unit (i.e. muropeptide). We show that several forms of muropeptides can stimulate growth resumption of dormantE. colicells, but the sugar – peptide bond is crucial for activity. We also demonstrate that muropeptides from several different species can induce growth resumption ofE. coliand alsoPseudomonas aeruginosa. These results, together with the previous identification of muropeptides as germination signal for bacterial spores, makes muropeptides rather universal cue for bacterial growth.
Importance of erythrocyte deformability for the alignment of malaria parasite upon invasion
Authors: Hillringhaus S. , Gompper G. , Fedosov D. A.
Published: April 2019

Invasion of erythrocytes by merozoites is an essential step for the survival and progression of malaria parasites. In order to invade red blood cells (RBCs), parasites have to adhere with their apex to the RBC membrane. Since a random adhesion contact between the parasite and membrane would be too inefficient, it has been hypothesized that merozoites are able to actively re-orient toward apex-membrane alignment. This is supported by several experimental observations which show that merozoites frequently induce considerable membrane deformations before the invasion process. Even though a positive correlation between RBC membrane deformation and successful invasion is established, the role of RBC mechanics and its deformation in the alignment process remains elusive. Using a mechanically realistic model of a deformable RBC, we investigate numerically the importance of RBC deformability for merozoite alignment. Adhesion between the parasite and RBC membrane is modeled by an attractive potential which might be inhomogeneous, mimicking possible adhesion gradients at the surface of a parasite. Our results show that RBC membrane deformations are crucial for successful merozoite alignment, and require strengths comparable to adhesion forces measured experimentally. Adhesion gradients along the parasite body further improve its alignment. Finally, an increased membrane rigidity is found to result in poor merozoite alignment, which can be a possible reason for the reduction in the invasion of RBCs in several blood diseases associated with membrane stiffening.

STATEMENT OF SIGNIFICANCE

Plasmodium parasites invade erythrocytes during the progression of malaria. To start invasion, the parasites have to re-orient themselves such that their apex establishes a direct contact with erythrocyte membrane. The re-orientation (or alignment) process is often associated with strong membrane deformations, which are believed to be induced by the parasite and are positively correlated with its alignment. We employ a mechanically realistic erythrocyte model to investigate the interplay of membrane deformations and merozoite alignment during parasite adhesion to an erythrocyte. Our model clearly demonstrates that erythrocyte membrane deformations are a key component of successful parasite alignment, since the re-orientation of parasites at rigidified membranes is generally poor. Therefore, our results suggest a possible mechanism for the reduction in erythrocyte invasion in several blood diseases associated with membrane stiffening.
Does parental angling selection affect the behavior or metabolism of brown trout parr?
Authors: Prokkola Jenni M. , Alioravainen Nico , Mehtätalo Lauri , Hyvärinen Pekka , Lemopoulos Alexandre , Metso Sara , Vainikka Anssi
Published: April 2019

The behavior of organisms can be subject to human induced selection such as that arising from fishing. Angling is expected to induce mortality on fish with bold and explorative behavior, which are behaviors commonly linked to a high standard metabolic rate. We studied the transgenerational response of brown trout (Salmo trutta) to angling-induced selection by examining the behavior and metabolism of 1-year-old parr between parents that were or were not captured by experimental fly fishing. We performed the angling selection experiment on both a wild and a captive population, and compared the offspring for standard metabolic rate and behavior under predation risk in common garden conditions. Angling had population-specific effects on risk taking and exploration tendency, but no effects on standard metabolic rate. Our study adds to the evidence that angling can induce transgenerational responses on fish personality. However, understanding the mechanisms of divergent responses between the populations requires further study on the selectivity of angling in various conditions.
Resveratrol prevents amyloid fibrillation of insulin by arresting it in a bioactive oligomeric form
Authors: Pathak Bani Kumar , Das Debajyoti , Bhakta Sayan , Chakrabarti Partha , Sengupta Jayati
Published: April 2019

Insulin fibrillation is a limiting factor for its long-term storage because of considerably reduced bioavailable moieties. Deposition of fibrillated insulin can also cause subcutaneous insulin amyloidoma. Toxic phenolic compounds along with Zinc are used during commercial preparation of insulin to stabilize it in a hexameric form. Designed or repurposed natural small molecules with anti-amyloidogenic properties could thus be attractive agents for preventing insulin fibrillation. Natural polyphenolic compounds which have been shown to serve as anti-amyloid agents for proteins associated with neurodegenerative diseases are potential candidates for such function.

In this study we have demonstrated that resveratrol, a natural polyphenol, can not only prevent insulin fibrillation but can also preserve insulin in a bioactive oligomeric form even at high temperature. While investigating the influence of some natural polyphenols on human insulin (hINS) in a condition inductive to amyloid fibrillation at physiological pH, we found attenuation, to different extents, of insulin fibril formation. However, visualization of polyphenol-treated hINS revealed that resveratrol in particular has the unique ability to arrest hINS before the onset of fibrillation growth in soluble oligomeric forms with discrete spherical morphology. Importantly, insulin treated with resveratrol retains its full biological activityin vivoand exerts no toxicity towards cell lines. Structural characterization of the major population of resveratrol-induced insulin oligomers by cryo-EM and single particle 3D reconstruction revealed its morphology that resembled crystal structure of insulin hexamer formulated with phenolic compounds. Thus, our study suggests that resveratrol can be an effective nontoxic substituent of phenolic compounds for insulin preservation.
BioSAXS measurements reveal that two antimicrobial peptides induce similar molecular changes in Gram-negative and Gram-positive bacteria
Authors: von Gundlach A.R. , Ashby M. , Gani J. , Lopez-Perez P. M. , Cookson A. , Huws S. , Rumancev C. , Garamus V.M. , Mikut R. , Rosenhahn A. , Hilpert K.
Published: April 2019

Two highly active short broad-spectrum AMPs (14D and 69D) with unknown mode of action have been investigated in regards to their effect against the Gram-negative bacteriaE. coliand the Gram-positive bacteria methicillin-resistantStaphylococcus aureus(MRSA). Minimal inhibitory concentration (MIC) measurements using a cell density of 108cfu/ml resulted in values between 16 and 32 μg/ml. Time kill experiments using 108cfu/ml revealed complete killing, except for 69D in combination with MRSA, where bacterial load was reduced a million times. Small angle X-ray scattering of biological samples (BioSAXS) at 108cfu/ml was applied to investigate the ultrastructural changes inE. coliand MRSA in response to these two broad-spectrum AMPs. In addition, electron microscopy (EM) was performed to visualize the treated and non-treated bacteria. As expected, the scattering curves generated using BioSAXS show the ultrastructure of the Gram-positive and Gram-negative bacteria to be very different (BioSAXS is not susceptible to the outer shape). After treatment with either peptide, the scattering curves ofE. coliand MRSA cells are much more alike. This data in conjunction with the EM indicates that ribosomes might be effected by the treatment as well as changes in the nucleoid occurs. Whereas in EM it is notoriously difficult to observe changes for spherical Gram-positives, the BioSAXS results are superior and reveal strongly similar effects for both peptides induced in Gram-positive as well as Gram-negative bacteria. Given the high-throughput possibility and robust statistics BioSAXS can support and speed up mode of action research in AMPs and other antimicrobial compounds, making a contribution towards the development of urgently needed drugs against resistant bacteria.
Intraspecific root and leaf trait variation with tropical forest successional status: consequences for community-weighted patterns
Authors: Hogan J. Aaron , Valverde-Barrantes Oscar J. , Ding Qiong , Xu Han , Baraloto Christopher
Published: April 2019

Quantifying the dimensions and magnitude of intraspecific root trait variation is key to understanding the functional trade-offs in the belowground plant strategies of tropical forest trees. Additionally, accurately measuring how belowground functional trait variation relates to soil environment and forest age is crucial to tropical forest modeling efforts.

We sampled leaf and root morphologies from 423 juvenile trees of 72 species from 14 Angiosperm families along a 6.6 km transect that corresponded to an environmental gradient in decreasing soil fertility and texture with increasing forest age.

We observed within-lineage conservative functional trait-shifts in root and leaf morphological traits along the transect. From secondary to primary forest, average leaf area increased 7 cm2and average root system diameter increased 0.4 mm. Mean specific leaf area decreased by 0.8 m2kg−1, specific root length decreased by 3.5 m kg−1, and root branching intensity decreased by 0.3 tips cm−1. Leaf thickness and root tissue density showed no change.

We coupled trait measurements to a network of 164 1/16th-ha plots across a Chinese tropical forest reserve, to scale individual trait measurements up to the community-level, accounting for forest age.

For most traits, intraspecific trait variation negatively covaried with species compositional turnover between plots in younger versus older forest to compound and create greater community-weighted differences in trait values than would be observed if intraspecific variation in traits with forest age was not accounted for.

SummaryRoot morphologies are variable with local scale variation in soil fertility and texture. Accurately understanding broader (i.e. forest)-scale patterns in root functional traits, requires attention to underlying environmental variation in soil resources, which interacts with environmental filtering of plant communities.
Auxin-mediated rapid degradation of selective proteins in hippocampal neurons
Authors: Nakano Risako , Ihara Naoki , Morikawa Shota , Nakashima Ai , Kanemaki Masato T. , Ikegaya Yuji , Takeuchi Haruki
Published: April 2019

Genetic manipulation of protein levels is a promising approach to identify the function of a specific protein in living organisms. Previous studies demonstrated that the auxin-inducible degron (AID) strategy provides rapid and reversible degradation of various proteins in fungi and mammalian mitotic cells. In this study, we employed this technology to postmitotic neurons to address whether the AID system could be applied to the nervous system. Using adeno-associated viruses, we simultaneously introduced EGFP fused with an AID tag, and an F-box family protein, TIR1 fromOryza sativa(OsTIR1) into hippocampal neurons. In dissociated hippocampal neurons, EGFP fluorescence signals rapidly decreased when adding a plant hormone, auxin. Further, auxin-induced EGFP degradation was also observed in hippocampal acute slices. Taken together, these results open the door for neuroscientists to manipulate protein expression levels by the AID-system in a temporally-controlled manner.
The conserved metalloprotease invadolysin is present in invertebrate haemolymph and vertebrate blood
Authors: Abhinav Kanishk , Feng Linda , Morrison Emma , Jung Yunshin , Dear James , Takahashi Satoru , Heck Margarete M. S.
Published: April 2019

We identified invadolysin, a novel essential metalloprotease, for functions in chromosome structure, cell proliferation and migration. Invadolysin also plays an important metabolic role in insulin signaling and is the only protease known to localise to lipid droplets, the main lipid storage organelle in the cell.In silicoexamination of the protein sequence of invadolysin predicts not only protease and lipase catalytic motifs, but also post-translational modifications and the secretion of invadolysin. Here we show that the protease motif of invadolysin is important for its role in lipid accumulation, but not in glycogen accumulation. The lipase motif does not appear to be functionally important for accumulation of lipids or glycogen. Post-translational modifications likely contribute to modulating the level, localisation or activity of invadolysin. We identified a secreted form of invadolysin in the soluble fraction of invertebrate hemolymph (where we observe sexually dimorphic forms) and also vertebrate plasma, including in the extracellular vesicle fraction. Biochemical analysis for various post-translational modifications demonstrated that secreted invadolysin is both N-and O-glycosylated, but not apparently GPI-linked. The discovery of invadolysin in the extracellular milieu suggests a role for invadolysin in normal organismal physiology.

Summary Statement

In this study, we show that the conserved metalloprotease invadolysin is present in invertebrate hemolymph and vertebrate blood, suggesting the protein may function in organismal physiology.
Transcriptional analysis identifies novel biomarkers associated with successful ex-vivo perfusion of human donor lungs
Authors: Ferdinand John R. , Morrison Morvern I. , Andreasson Anders , Charlton Catriona , Chhatwal Alisha , Scott William E. , Borthwick Lee A. , Clatworthy Menna R. , Fisher Andrew J.
Published: April 2019

Transplantation is an effective treatment for end-stage lung disease but donor organ shortage is a major problem. Ex-vivo lung perfusion (EVLP) of marginal organs enables functional assessment under normothermic conditions to facilitate clinical decision-making around utilisation, but the molecular processes occurring during EVLP, and how they differ between more or less viable lungs, remains to be determined. Here we used RNA sequencing to delineate changes in gene expression occurring in n=10 donor lungs undergoing EVLP, comparing lungs that were deemed transplantable (n=6) to those deemed unusable (n=4). We found that lungs deemed suitable for transplantation following EVLP had reduced induction of a number of innate immune pathways during EVLP, but a greater increase in genes involved in oxidative phosphorylation, a critical ATP-degenerating pathway. Furthermore, SCGB1A1, a gene encoding an anti-inflammatory secretoglobin CC10, and other club cell genes were significantly increased in transplantable lungs following perfusion, whilst CHIT-1 was decreased. Using a larger validation cohort (n=18), we confirmed that the ratio of CHIT1 and SCGB1A1 protein levels in lung perfusate have potential utility to distinguish transplantable and non-transplantable lungs (AUC 0.81). Together, our data identify novel biomarkers that may assist with pre-transplant lung assessment, as well as pathways that may amenable to therapeutic intervention during EVLP.

Single sentence summary

Transcriptional changes in lungs undergoing ex vivo normothermic perfusion identify chitinase1 and club cell genes as potential biomarkers to guide utilisation
Identifying site- and stimulation-specific TMS-evoked EEG potentials using a quantitative cosine similarity metric
Authors: Freedberg Michael , Reeves Jack A. , Hussain Sara J. , Zaghloul Kareem A. , Wassermann Eric M.
Published: April 2019

The ability to interpret transcanial magnetic stimulation (TMS) evoked EEG potentials (TEPs) is limited by artifacts, such as auditory evoked responses produced by the TMS coil. TEPs generated from direct cortical stimulation should vary in spatial distribution with stimulation site and from responses to sham stimulation. Responses that do not show these effects are likely to be artifactual. In 20 healthy volunteers, we delivered active and sham TMS to right prefrontal, left primary motor, and left posterior parietal cortex and compared the waveform similarity of TEPs between stimulation sites and active and sham TMS with a cosine similarity-based analysis method. We looked for epochs after the stimulus when the spatial pattern of TMS-evoked activation had greater than random similarity between stimulation sites and sham vs. active TMS, indicating presence of a dominant artifact, such as the auditory brain response. We calculated and binarized the derivatives of the TEPs recorded from 30 EEG channels and calculated cosine similarity between conditions at each time point with millisecond resolution. Only TEP components occurring before approximately 80 ms differed across stimulation sites and between active and sham, indicating site and condition-specific responses. TEP components before about 80 ms can be safely interpreted as stimulation location-specific responses to TMS, but components beyond this latency should be interpreted with caution due to high similarity in their spatial distribution.
Spatio-Temporal Dynamics of Landscape Use by the BumblebeeBombus atratus(Hymenoptera: Apidae) and its relationship with pollen provisioning
Authors: Cavigliasso Pablo , Phifer Colin C. , Adams Erika M. , Flaspohler David , Gennari Gerardo P. , Licata Julian A. , Chacoff Natacha P.
Published: April 2019

Understanding how bees use resources at a landscape scale is essential for developing meaningful management plans that sustain populations and the pollination services they provide. Bumblebees are important pollinators for many wild and cultivated plants, and have experienced steep population declines worldwide. Bee foraging behavior can be influenced by resource availability and the bee’s lifecycle stage. To better understand these relationships, we studied the habitat selection ofBombus atratusby tracking 17 queen bumblebees with radio telemetry in blueberry fields in Entre Ríos province, Argentina. To evaluate land use and floral resources used by bumblebees, we tracked bees before and after nest establishment and estimated home ranges using minimum convex polygons and kernel density methods. We also classify the pollen of their body to determine which botanical resources they use from the floral species available. We characterized land use for each bee as the relative proportion of GPS points inside of each land use. Bumblebees differed markedly in their movement behavior in relation to nest establishment. They moved over larger areas and mostly within blueberry fields before to nest establishment, in contrast to after establishing the nest that they preferred the edges near forest plantations and changed the nutritional resources by wild floral species. Our study is the first to track queen bumblebee movements in an agricultural setting and relate movement change across time and space with pollen resource availability. This study provides insight into the way bumblebee queens use different habitat elements at crucial periods in their lifecycle, showing the importance of mass flowering crops like blueberry in the first stages of queen’s lifecycle and how diversified landscapes help support bee populations as their needs changes during different phases of their lifecycle.
Cadmium(II) three-dimensional coordination polymers constructed from 1,3,5-tris(4-carboxyphenoxy)benzene: synthesis, crystal structure, fluorescence and I2 sorption characterization
Authors: Bai Yuting , Han Meirong , Wu Enxi , Feng Sisi , Zhu Miaoli
Published: April 2019

Two three-dimensional (3D) CdII coordination polymers, namely poly[[di-μ-aqua-diaquabis{μ5-4,4′,4′′-[benzene-1,3,5-triyltris(oxy)]tribenzoato}tricadmium(II)] dihydrate], {[Cd3(C27H15O9)2(H2O)4]·2H2O}
n
, (I), and poly[[aqua{μ6-4,4′,4′′-[benzene-1,3,5-triyltris(oxy)]tribenzoato}(μ-formato)[μ-1,1′-(1,4-phenylene)bis(1H-imidazole)]dicadmium(II)] dihydrate], {[Cd2(C27H15O9)(C12H10N4)(HCOO)(H2O)]·2H2O}
n
, (II), have been hydrothermally synthesized from the reaction system containing Cd(NO3)2·4H2O and the flexible tripodal ligand 1,3,5-tris(4-carboxyphenoxy)benzene (H3tcpb) via tuning of the auxiliary ligand. Both complexes have been characterized by single-crystal X-ray diffraction analysis, elemental analysis, IR spectra, powder X-ray diffraction and thermogravimetric analysis. Complex (I) is a 3D framework constructed from trinuclear structural units and tcpb3− ligands in a μ5-coordination mode. The central CdII atom of the trinuclear unit is located on a crystallographic inversion centre and adopts an octahedral geometry. The metal atoms are bridged by four syn–syn carboxylate groups and two μ2-water molecules to form trinuclear [Cd3(COO)4(μ2-H2O)2] secondary building units (SBUs). These SBUs are incorporated into clusters by bridging carboxylate groups to produce pillars along the c axis. The one-dimensional inorganic pillars are connected by tcpb3− linkers in a μ5-coordination mode, thus forming a 3D network; its topology corresponds to the point symbol (42.62.82)(44.62)2(45.66.84)2. In contrast to (I), complex (II) is characterized by a 3D framework based on dinuclear cadmium SBUs, i.e. [Cd2(COO)3]. The two symmetry-independent CdII ions display different coordinated geometries, namely octahedral [CdN2O4] and monocapped octahedral [CdO7]. The dinuclear SBUs are incorporated into clusters by bridging formate groups to produce pillars along the c axis. These pillars are further bridged either by tcpb3− ligands into sheets or by 1,4-bis(imidazol-1-yl)benzene ligands into undulating layers, and finally these two-dimensional surfaces interweave, forming a 3D structure with the point symbol (4.62)(47.614). Compound (II) exhibits reversible I2 uptake of 56.8 mg g−1 with apparent changes in the visible colour and the UV–Vis and fluorescence spectra, and therefore may be regarded as a potential reagent for the capture and release of I2.
Developing a Scratch-based coding achievement test
Authors: Demir Ömer , Seferoğlu Süleyman Sadi
Published: April 2019

Purpose

The lack of a reliable and valid measurement tool for coding achievement emerges as a major problem in Turkey. Therefore, the purpose of this study is to develop a Scratch-based coding achievement test.

Design/methodology/approach

Initially, an item pool with 31 items was created. The item pool was classified within the framework of Bayman and Mayer’s (1988) types of coding knowledge to support content validity of the test. Then the item pool was applied to 186 volunteer undergraduates at Hacettepe University during the spring semester of the 2017-2018 academic year. Subsequently, the item analysis was conducted for construct validity of the test.

Findings

In all, 13 items were discarded from the test, leaving a total of 18 items. Out of the 18-item version of the coding achievement test, 4, 5 and 9 items measured syntactic, conceptual and strategic knowledge, respectively, among the types of coding knowledge. Furthermore, average item discrimination index (0.531), average item difficulty index (0.541) and Cronbach Alpha reliability coefficient (0.801) of the test were calculated.

Practical implications

Scratch users, especially those who are taking introductory courses at Turkish universities, could benefit from a reliable and valid coding achievement test developed in this study.

Originality/value

This paper has theoretical and practical value, as it provides detailed developmental stages of a reliable and valid Scratch-based coding achievement test.
Experimental verification of textured mechanical seal designed using multi-objective optimization
Authors: Wang Xiuying , Khonsari Michael , Li Siyuan , Dai Qingwen , Wang Xiaolei
Published: April 2019

Purpose

This study aims to simultaneously enhance the load-carrying capacity and control the leakage rate of mechanical seals by optimizing the texture shape.

Design/methodology/approach

A multi-objective optimization approach is implemented to determine the optimal “free-form” textures and optimal circular dimples. Experiments are conducted to validate the simulation results.

Findings

The experimental coefficient of friction (COF) and leakage rate are in good agreement with the calculated results. In addition, the optimal “free-form” texture shows a lower COF and a lower leakage in most cases.

Originality/value

This work provides a method to optimize the surface texture for a better combination performance of mechanical seals.