bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractWhen 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

ABSTRACTInvasion 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 SIGNIFICANCEPlasmodium 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

AbstractThe 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

AbstractInsulin 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

AbstractTwo 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

SummaryQuantifying 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

AbstractGenetic 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

AbstractWe 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 StatementIn 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

AbstractTransplantation 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 summaryTranscriptional 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

AbstractThe 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

AbstractUnderstanding 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.
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.