bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying hetero-protein complexes in the nuclear envelope
Authors: Hennen J. , Hur K.H. , Kohler J. , Karuka S.R. , Angert I. , Luxton G.W.G. , Mueller J.D.
Published: July 2019

The nucleus is delineated by the nuclear envelope (NE), which is a double membrane barrier composed of the inner and outer nuclear membranes as well as a ~40 nm wide lumen. In addition to its barrier function, the NE acts as a critical signaling node for a variety of cellular processes which are mediated by protein complexes within this subcellular compartment. While fluorescence fluctuation spectroscopy (FFS) is a powerful tool for characterizing protein complexes in living cells, it was recently demonstrated that conventional FFS methods are not suitable for applications in the NE because of the presence of slow nuclear membrane undulations. We previously addressed this challenge by developing time-shifted mean-segmented Q (tsMSQ) analysis and applied it to successfully characterize protein homo-oligomerization in the NE. However, many NE complexes, such as the linker of the nucleoskeleton and cytoskeleton (LINC) complex, are formed by heterotypic interactions, which single-color tsMSQ is unable to characterize. Here, we describe the development of dual-color (DC) tsMSQ to analyze NE hetero-protein complexes built from proteins that carry two spectrally distinct fluorescent labels. Experiments performed on model systems demonstrate that DC tsMSQ properly identifies hetero-protein complexes and their stoichiometry in the NE by accounting for spectral crosstalk and local volume fluctuations. Finally, we applied DC tsMSQ to study the assembly of the LINC complex, a hetero-protein complex composed of Klarsicht/ANC-1/SYNE homology (KASH) and Sad1/UNC-84 (SUN) proteins, in the NE of living cells. Using DC tsMSQ, we demonstrate the ability of the SUN protein SUN2 and the KASH protein nesprin-2 to form a hetero-complexin vivo. Our results are consistent with previously publishedin vitrostudies and demonstrate the utility of the DC tsMSQ technique for characterizing NE hetero-protein complexes.

Statement of Significance

Protein complexes found within the nuclear envelope (NE) play a vital role in regulating cellular functions ranging from gene expression to cellular movement. However, the assembly state of these complexes within their native environment remains poorly understood, which is compounded by a general lack of fluorescence techniques suitable for quantifying the oligomeric state of NE protein complexes. This study aims at addressing this issue by introducing dual-color time-shifted mean-segmented Q analysis as a fluorescence fluctuation method specifically designed to identify the average oligomeric state of hetero-protein complexes within the NE of living cells.
Interaction Between Ploidy, Breeding System, and Lineage Diversification
Authors: Zenil-Ferguson Rosana , Burleigh J. Gordon , Freyman William A. , Igić Boris , Mayrose Itay , Goldberg Emma E.
Published: July 2019

If particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be understood as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversification rate differences is complicated by the wide variety of characters under consideration and the statistical challenges of testing for associations from comparative phylogenetic data. Ploidy (diploid vs. polyploid states) and breeding system (self-incompatible vs. self-compatible states) have been repeatedly suggested as possible drivers of differential diversification. We investigate the connections of these traits, including their interaction, to speciation and extinction rates in Solanaceae. We show that the effect of ploidy on diversification can be largely explained by its correlation with breeding system and that additional unknown factors, alongside breeding system, influence diversification rates. These results are largely robust to allowing for diploidization. Finally, we find that the most common evolutionary pathway to polyploidy in Solanaceae occurs via direct breakdown of self-incompatibility by whole genome duplication, rather than indirectly via breakdown followed by polyploidization.
Neural evidence for the prediction of animacy features during language comprehension: Evidence from MEG and EEG Representational Similarity Analysis
Authors: Wang Lin , Wlotko Edward , Alexander Edward , Schoot Lotte , Kim Minjae , Warnke Lena , Kuperberg Gina R.
Published: July 2019

It has been proposed that people can generate probabilistic predictions at multiple levels of representation during language comprehension. We used Magnetoencephalography (MEG) and Electroencephalography (EEG), in combination with Representational Similarity Analysis (RSA), to seek neural evidence for the prediction of animacy features. In two studies, MEG and EEG activity was measured as human participants (both sexes) read three-sentence scenarios. Verbs in the final sentences constrained for either animate or inanimate semantic features of upcoming nouns, and the broader discourse context constrained for either a specific noun or for multiple nouns belonging to the same animacy category. We quantified the similarity between spatial patterns of brain activity following the verbs until just before the presentation of the nouns. The MEG and EEG datasets revealed converging evidence that the similarity between spatial patterns of neural activity following animate constraining verbs was greater than following inanimate constraining verbs. This effect could not be explained by lexical-semantic processing of the verbs themselves. We therefore suggest that it reflected the inherent difference in the semantic similarity structure of the predicted animate and inanimate nouns. Moreover, the effect was present regardless of whether a specific word could be predicted, providing strong evidence for the prediction of coarse-grained semantic features that goes beyond the prediction of individual words.

Significance statement

Language inputs unfold very quickly during real-time communication. By predicting ahead we can give our brains a “head-start”, so that language comprehension is faster and more efficient. While most contexts do not constrain strongly for a specific word, they do allow us to predict some upcoming information. For example, following the context, “they cautioned the…”, we can predict that the next word will be animate rather than inanimate (we can caution a person, but not an object). Here we used EEG and MEG techniques to show that the brain is able to use these contextual constraints to predict the animacy of upcoming words during sentence comprehension, and that these predictions are associated with specific spatial patterns of neural activity.
BIRD: Identifying Cell Doublets via Biallelic Expression from Single cells
Authors: Wainer-Katsir Kerem , Linial Michal
Published: July 2019

Motivation

Current technologies for single-cell transcriptomics allow thousands of cells to be analyzed in a single experiment. The increased scale of these methods led to a higher risk of cell doublets’ contamination. Available tools and algorithms for identifying doublets and estimating their occurrence in single-cell expression data focus on cell doublets from different species, cell types or individuals.

Results

In this study, we analyze transcriptomic data from single cells having an identical genetic background. We claim that the ratio of monoallelic to biallelic expression provides a discriminating power towards doublets’ identification. We present a pipeline called BIRD (BIallelic Ratio for Doublets) that relies on heterologous genetic variations extracted from single-cell RNA-seq (scRNA-seq). For each dataset, doublets were artificially created from the actual data and used to train a predictive model. BIRD was applied on Smart-Seq data from 163 primary fibroblasts. The model achieved 100% accuracy in annotating the randomly simulated doublets. Bonafide doublets from female-origin fibroblasts were verified by the unexpected biallelic expression from X-chromosome. Data from 10X Genomics microfluidics of peripheral blood cells analyzed by BIRD achieved in average 83% (± 3.7%) accuracy with an area under the curve of 0.88 (± 0.04) for a collection of ∼13,300 single cells.

Conclusions

BIRD addresses instances of doublets which were formed from cell mixtures of identical genetic background and cell identity. Maximal performance is achieved with high coverage data. Success in identifying doublets is data specific which varies according to the experimental methodology, genomic diversity between haplotypes, sequence coverage, and depth.
Conjunctive representation of what and when in monkey hippocampus and lateral prefrontal cortex during an associative memory task
Authors: Cruzado Nathanael A. , Tiganj Zoran , Brincat Scott L. , Miller Earl K. , Howard Marc W.
Published: July 2019

Adaptive memory requires the organism to form associations that bridge between events separated in time. Many studies show interactions between hippocampus (HPC) and prefrontal cortex (PFC) during formation of such associations. We analyze neural recording from monkey HPC and PFC during a memory task that requires the monkey to associate stimuli separated by about a second in time. After the first stimulus was presented, large numbers of units in both HPC and PFC fired in sequence. Many units fired only when a particular stimulus was presented at a particular time in the past. These results indicate that both HPC and PFC maintain a temporal record of events that could be used to form associations across time. This temporal record of the past is a key component of the temporal coding hypothesis, a hypothesis in psychology that memory not only encodes what happened, but when it happened.
Rational Design of a Protein Kinase A Nuclear-cytosol Translocation Reporter
Authors: Kim Allen K. , Wu Helen D. , Inoue Takanari
Published: July 2019

Protein Kinase A (PKA) exists as a tetrameric holoenzyme which activates with increase of cAMP and plays an important role in many physiological processes including cardiac physiology, neuronal development, and adipocyte function. Although this kinase has been the subject of numerous biosensor designs, a single-fluorophore reporter that performs comparably to Förster resonance energy transfer (FRET) has not yet been reported. Here, we have used basic observations of electrostatic interactions in PKA substrate recognition mechanism and nucleus localization sequence motif to design a phosphorylation switch that shuttles between the cytosol and the nucleus, a strategy that should be generalizable to all basophilic kinases. The resulting reporter yielded comparable kinetics and dynamic range to the PKA FRET reporter, AKAR3EV. We also performed basic characterization and demonstrated its potential use in monitoring multiple signaling molecules inside cells using basic fluorescence microscopy. Due to the single-fluorophore nature of this reporter, we envision that this could find broad applications in studies involving single cell analysis of PKA activity.
An Optimally Weighted Combination Method to Detect Novel Disease Associated Genes Using Publicly Available GWAS Summary Data
Authors: Zhang Jianjun , Gonzales Samantha , Liu Jianguo , Gao Xiaoyi Raymond , Wang Xuexia
Published: July 2019

Gene-based analyses offer a useful alternative and complement to the usual single nucleotide polymorphism (SNP) based analysis for genome-wide association studies (GWASs). Using appropriate weights (pre-specified or eQTL-derived) can boost statistical power, especially for detecting weak associations between a gene and a trait. Because the sparsity level or association directions of the underlying association patterns in real data are often unknown and access to individual-level data is limited, we propose an optimal weighted combination (OWC) test applicable to summary statistics from GWAS. This method includes burden tests, weighted sum of squared score (SSU), weighted sum statistic (WSS), and the score test as its special cases. We analytically prove that aggregating the variants in one gene is the same as using the weighted combination of Z-scores for each variant based on the score test method. We also numerically illustrate that our proposed test outperforms several existing comparable methods via simulation studies. Lastly, we utilize schizophrenia GWAS data and a fasting glucose GWAS meta-analysis data to demonstrate that our method outperforms the existing methods in real data analyses. Our proposed test is implemented in the R program OWC, which is freely and publicly available.
Comparative analysis of the CDR loops of antigen receptors
Authors: Wong Wing Ki , Leem Jinwoo , Deane Charlotte M.
Published: July 2019

The adaptive immune system uses two main types of antigen receptors: T-cell receptors (TCRs) and antibodies. While both proteins share a globally similar β-sandwich architecture, TCRs are specialised to recognise peptide antigens in the binding groove of the major histocompatibility complex, while antibodies can bind an almost infinite range of molecules. For both proteins, the main determinants of target recognition are the complementarity-determining region (CDR) loops. Five of the six CDRs adopt a limited number of backbone conformations, known as the ‘canonical classes’; the remaining CDR (β3 in TCRs and H3 in antibodies) is more structurally diverse. In this paper, we first update the definition of canonical forms in TCRs, build an auto-updating sequence-based prediction tool (available at http://opig.stats.ox.ac.uk/resources) and demonstrate its application on large scale sequencing studies. Given the global similarity of TCRs and antibodies, we then examine the structural similarity of their CDRs. We find that TCR and antibody CDRs tend to have different length distributions, and where they have similar lengths, they mostly occupy distinct structural spaces. In the rare cases where we found structural similarity, the underlying sequence patterns for the TCR and antibody version are different. Finally, where multiple structures have been solved for the same CDR sequence, the structural variability in TCR loops is higher than that in antibodies, suggesting TCR CDRs are more flexible. These structural differences between TCR and antibody CDRs may be important to their different biological functions.
Representational organization of novel task sets during proactive encoding
Authors: Palenciano Ana F. , González-García Carlos , Arco Juan E. , Pessoa Luiz , Ruz María
Published: July 2019

Recent multivariate analyses of brain data have boosted our understanding of the organizational principles that shape neural coding. However, most of this progress has focused on perceptual visual regions (Connolly et al., 2012), whereas far less is known about the organization of more abstract, action-oriented representations. In this study, we focused on humans’ remarkable ability to turn novel instructions into actions. While previous research shows that instruction encoding is tightly linked to proactive activations in fronto-parietal brain regions, little is known about the structure that orchestrates such anticipatory representation. We collected fMRI data while participants (both males and females) followed novel complex verbal rules that varied across control-related variables (integrating within/across stimuli dimensions, response complexity, target category) and reward expectations. Using Representational Similarity Analysis (Kriegeskorte et al., 2008) we explored where in the brain these variables explained the organization of novel task encoding, and whether motivation modulated these representational spaces. Instruction representations in the lateral prefrontal cortex were structured by the three control-related variables, while intraparietal sulcus encoded response complexity and the fusiform gyrus and precuneus organized its activity according to the relevant stimulus category. Reward exerted a general effect, increasing the representational similarity among different instructions, which was robustly correlated with behavioral improvements. Overall, our results highlight the flexibility of proactive task encoding, governed by distinct representational organizations in specific brain regions. They also stress the variability of motivation-control interactions, which appear to be highly dependent on task attributes such as complexity or novelty.

Significance Statement

In comparison with other primates, humans display a remarkable success in novel task contexts thanks to our ability to transform instructions into effective actions. This skill is associated with proactive task-set reconfigurations in fronto-parietal cortices. It remains yet unknown, however, how the brain encodes in anticipation the flexible, rich repertoire of novel tasks that we can achieve. Here we explored cognitive control and motivation-related variables that might orchestrate the representational space for novel instructions. Our results showed that different dimensions become relevant for task prospective encoding depending on the brain region, and that the lateral prefrontal cortex simultaneously organized task representations following different control-related variables. Motivation exerted a general modulation upon this process, diminishing rather than increasing distances among instruction representations.
Chloride dynamics alter the input-output properties of neurons
Authors: Currin Christopher B. , Trevelyan Andrew J. , Akerman Colin J. , Raimondo Joseph V.
Published: July 2019

Fast synaptic inhibition is a critical determinant of neuronal output, with subcellular targeting of synaptic inhibition able to exert different transformations of the neuronal input-output function. At the receptor level, synaptic inhibition is primarily mediated by chloride-permeable Type A GABA receptors. Consequently, dynamics in the neuronal chloride concentration can alter the functional properties of inhibitory synapses. How differences in the spatial targeting of inhibitory synapses interact with intracellular chloride dynamics to modulate the input-output function of neurons is not well understood. To address this, we developed computational models of multi-compartment neurons that incorporate experimentally parametrised mechanisms to account for neuronal chloride influx, diffusion, and extrusion. We found that synaptic input (either excitatory, inhibitory, or both) can lead to subcellular variations in chloride concentration, despite a uniform distribution of chloride extrusion mechanisms. Accounting for chloride changes resulted in substantial alterations in the neuronal input-output function. This was particularly the case for peripherally targeted dendritic inhibition where dynamic chloride compromised the ability of inhibition to offset neuronal input-output curves. Our simulations revealed that progressive changes in chloride concentration mean that the neuronal input-output function is not static but varies significantly as a function of the duration of synaptic drive. Finally, we found that the observed effects of dynamic chloride on neuronal output were entirely mediated by changes in the dendritic reversal potential for GABA. Our findings provide a framework for understanding the computational effects of chloride dynamics on dendritically targeted synaptic inhibition.

Author Summary

The fundamental unit of computation in the brain is the neuron, whose output reflects information within the brain. A determining factor in the transfer and processing of information in the brain is the modulation of activity by inhibitory synaptic inputs. Fast synaptic inhibition is mediated by the neurotransmitter GABA binding to GABAA receptors, which are permeable to chloride ions. How changes in chloride ion concentration affect neuronal output is an important consideration for information flow in the brain that is currently not being thoroughly investigated. In this research, we used multi-compartmental models of neurons to link the deleterious effects that accumulation of chloride ions can have on inhibitory signalling with changes in neuronal ouput. Together, our results highlight the importance of accounting for changes in chloride concentration in theoretical and computer-based models that seek to explore the computational properties of inhibition.
Laminar differences in responses to naturalistic texture in macaque V1 and V2
Authors: Ziemba Corey M , Perez Richard K , Pai Julia , Hallum Luke E , Shooner Christopher , Kelly Jenna G , Movshon J Anthony
Published: July 2019

Most single units recorded from macaque V2 respond with higher firing rates to synthetic texture images containing “naturalistic” higher-order statistics than to spectrally matched “noise” images lacking these statistics. In contrast, few single units in V1 show this property. We explored how the strength and dynamics of response vary across the different layers of visual cortex by recording multiunit and gamma band activity evoked by brief presentations of naturalistic and noise images in V1 and V2 of anesthetized macaque monkeys. As previously reported, recordings in V2 showed consistently stronger responses to naturalistic texture than to spectrally matched noise. In contrast to single unit recordings, V1 multiunit activity showed some preference for images with naturalistic statistics, and in gamma band activity this preference was comparable across V1 and V2. Sensitivity to naturalistic image structure was strongest in the supragranular and infragranular layers of V1, but weak in granular layers, suggesting that it might reflect feedback from V2. Response timing was consistent with this idea. Visual responses appeared first in V1, followed by V2. Sensitivity to naturalistic texture emerged first in V2, followed by the supragranular and infragranular layers of V1, and finally in the granular layers of V1. Our results demonstrate laminar differences in the encoding of higher-order statistics of natural texture, and suggest that this sensitivity first arises in V2 and is fed back to modulate activity in V1.

Significance Statement

The circuit mechanisms responsible for visual representations of intermediate complexity are largely unknown. We used a well-validated set of synthetic texture stimuli to probe the temporal and laminar profile of sensitivity to the higher-order statistical structure of natural images. We found that this sensitivity emerges first and most strongly in V2 but soon after in V1. However, sensitivity in V1 is higher in the laminae (extragranular) and recording modalities (local field potential) most likely affected by V2 connections, suggesting a feedback origin. Our results show how sensitivity to naturalistic image structure emerges across time and circuitry in the early visual cortex.
Globally elevating the AGE clearance receptor, OST48, does not protect against the development of diabetic kidney disease, despite improving insulin secretion
Authors: Zhuang Aowen , Yap Felicia YT , McCarthy Domenica , Leung Sherman S. , Penfold Sally A. , Leung Chris , Sourris Karly C. , Harcourt Brooke E. , Thallas-Bonke Vicki , Coughlan Melinda T , Schulz Benjamin L , Forbes Josephine M
Published: July 2019

The accumulation of advanced glycation end products (AGEs) have been implicated in the development and progression of diabetic kidney disease (DKD). There has been interest in investigating the potential of AGE clearance receptors, such as oligosaccharyltransferase-48kDa subunit (OST48) to prevent the detrimental effects of excess AGE accumulation seen in the diabetic kidney. Here the objective of the study was to increase the expression of OST48 to examine if this slowed the development of DKD by facilitating the clearance of AGEs. Groups of 8-week-old heterozygous knock-in male mice (n=9-12/group) over-expressing the gene encoding for OST48, dolichyl-diphosphooligosaccharide-protein glycosyltransferase (DDOST+/-) and litter mate controls were randomised to either (i) no diabetes or (ii) diabetes induced via multiple low-dose streptozotocin and followed for 24 weeks. By the study end, global over expression of OST48 increased glomerular OST48. This facilitated greater renal excretion of AGEs but did not affect circulating or renal AGE concentrations. Diabetes resulted in kidney damage including lower glomerular filtration rate, albuminuria, glomerulosclerosis and tubulointerstitial fibrosis. In diabetic mice, tubulointerstitial fibrosis was further exacerbated by global increases in OST48. There was significantly insulin effectiveness, increased acute insulin secretion, fasting insulin concentrations and AUCinsulin observed during glucose tolerance testing in diabetic mice with global elevations in OST48 when compared to diabetic wild-type littermates. Overall, this study suggested that despite facilitating urinaryrenal AGE clearance, there were no benefits observed on kidney functional and structural parameters in diabetes afforded by globally increasing OST48 expression. However, the improvements in insulin secretion seen in diabetic mice with global over-expression of OST48 and their dissociation from effects on kidney function warrant future investigation.
A neuromechanical model of multiple network rhythmic pattern generators for forward locomotion inC. elegans
Authors: Olivares Erick , Izquierdo Eduardo J. , Beer Randall D.
Published: July 2019

Multiple mechanisms contribute to the generation, propagation, and coordination of the rhythmic patterns necessary for locomotion inCaenorhabditis elegans. Current experiments have focused on two possibilities: pacemaker neurons and stretch-receptor feedback. Here, we focus on whether it is possible that a chain of multiple network rhythmic pattern generators in the ventral nerve cord also contribute to locomotion. We use a simulation model to search for parameters of the anatomically constrained ventral nerve cord circuit that, when embodied and situated, can drive forward locomotion on agar, in the absence of pacemaker neurons or stretch-receptor feedback. Systematic exploration of the space of possible solutions reveals that there are multiple configurations that result in locomotion that is consistent with certain aspects of the kinematics of worm locomotion on agar. Analysis of the best solutions reveals that gap junctions between different classes of motorneurons in the ventral nerve cord can play key roles in coordinating the multiple rhythmic pattern generators.
Lessons in genome engineering: opportunities, tools and pitfalls
Authors: Poernbacher Ingrid , Crossman Sam , Kurth Joachim , Nojima Hisashi , Baena-Lopez Alberto , Alexandre Cyrille , Vincent Jean-Paul
Published: July 2019

CRISPR/Cas technology allows the creation of double strand breaks and hence loss of function mutations at any location in the genome. This technology is now routine for many organisms and cell lines. Here we describe how CRISPR/Cas can be combined with other DNA manipulation techniques (e.g. homology-based repair, site-specific integration and Cre or FLP-mediated recombination) to create sophisticated tools to measure and manipulate gene activity. In one class of applications, a single site-specific insertion generates a transcriptional reporter, a loss-of function allele, and a tagged allele. In a second class of modifications, essential sequences are deleted and replaced with an integrase site, which serves as a platform for the creation of custom reporters, transcriptional drivers, conditional alleles and regulatory mutations. We describe how these tools and protocols can be implemented easily and efficiently. Importantly, we also highlight unanticipated failures, which serve as cautionary tales, and suggest mitigating measures. Our tools are designed for use inDrosophilabut the lessons we draw are likely to be widely relevant.

AUTHOR SUMMARY

The genome contains all the information that an organism needs to develop and function throughout its life. One of the goal of genetics is to decipher the role of all the genes (typically several thousands for an animal) present in the genome. One approach is to delete each gene and assay the consequences. Deletion of individual genes is now readily achieved with a technique called CRISPR/Cas9. However, simple genetic deletion provides limited information. Here we describe strains and DNA vectors that streamline the generation of more sophisticated genetic tools. We describe general means of creating alleles (genetic variants) that enable gene activity to be measured and experimentally modulated in space and time. Although the tools we describe are universally applicable, each gene requires special consideration. Based on our experience of successes and failures, we suggest measures to maximise the chances that engineered alleles serve their intended purpose. Although our methods are designed for use in Drosophila, they could be adapted to any organism that is amenable to CRISPR/Cas9 genome modification.
Unilateral neglect is associated with poor proprioception after stroke – a systematic review
Authors: Fisher Georgia , de Oliveira Camila Quel , Gandevia Simon , Kennedy David
Published: July 2019

Background

Proprioceptive impairment is a potential contributing factor to the clinical presentation of Unilateral Neglect (UN), a common and debilitating condition that can occur after stroke. To date there has not been a comprehensive review of studies examining the various aspects of proprioception in UN after stroke.

Aim

To determine if the presence of UN is associated with more severe proprioceptive deficit in stroke affected populations.

Methods

The MEDLINE, Embase, Scopus, CINAHL and Web of Science databases were searched from inception to January 2019 using an a priori search strategy. Two independent reviewers screened abstracts and full texts. Two reviewers then independently extracted data from each full text. A third reviewer resolved disagreements at each step. Risk of bias was assessed using the AXIS Quality Assessment tool. For full protocol see PROSPERO, registration number CRD42018086070. One-hundred and sixty-seven abstracts were identified, of which fifty-four were eligible for full text screening. A total of 18 papers were included in the review.

Conclusions

More severe proprioceptive deficit is associated with the presence of UN after stroke. However, the available evidence is limited by the large heterogeneity of assessment of both UN and proprioception, and level of study quality. UN and proprioception are seldom completely assessed in research, and it is likely this is true in everyday clinical practice.
Exploring the basis of 2-propenyl and 3-butenyl glucosinolate synthesis by QTL mapping and RNA-sequencing in Brassica juncea
Authors: Khattak Aimal Nawaz , Wang Tianya , Yu Kunjiang , Yang Renqin , Wan Wei , Ye Botao , Tian Entang
Published: July 2019

Brassica juncea is used as a condiment, as vegetables and as an oilseed crop, especially in semiarid areas. In the present study, we constructed a genetic map using one recombinant inbred line (RIL) of B. juncea. A total of 304 ILP (intron length polymorphism) markers were mapped to 18 linkage groups designated LG01-LG18 in B. juncea. The constructed map covered a total genetic length of 1671.13 cM with an average marker interval of 5.50 cM. The QTLs for 2-propenyl glucosinolates (GSLs) colocalized with the QTLs for 3-butenyl GSLs between At1g26180 and BnapPIP1580 on LG08 in the field experiments of 2016 and 2017. These QTLs accounted for an average of 42.3% and 42.6% phenotypic variation for 2-propenyl and 3-butenyl GSLs, respectively. Furthermore, the Illumina RNA-sequencing technique was used to excavate the genes responsible for the synthesis of GSLs in the siliques of the parental lines of the RIL mapping population, because the bulk of the seed GSLs might originate from the siliques. Comparative analysis and annotation by gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) revealed that 324 genes were involved in GSL metabolism, among which only 24 transcripts were differentially expressed genes (DEGs). Among those DEGs, 15 genes were involved in the biosynthesis and transport of aliphatic GSLs, and their expression patterns were further validated by qRT-PCR analysis. These RNA-Seq results will be helpful for further fine mapping, gene cloning and genetic mechanisms of 2-propenyl and 3-butenyl GSLs in B. juncea.
Microstructure and water distribution in catalysts for polymer electrolyte fuel cells, elucidated by contrast variation small-angle neutron scattering
Authors: Koizumi Satoshi , Ueda Satoru , Inada Takumi , Noda Yohei , Robinson Robert A.
Published: July 2019

By using small-angle neutron scattering (SANS) reinforced by scanning electron microscopy, the fine structure of catalysts for polymer electrolyte fuel cells has been investigated. The experimental data resulting from contrast variation with mixed light and heavy water (H2O/D2O) are well described by a core–shell model with fluctuations in concentration between water and Nafion. In particular, SANS obtained with the mixed water ratio 30/70, which corresponds to a matching point between mixed water and Nafion, shows a broad scattering maximum, which is attributed to a 5 nm-thick Nafion shell on the surface of the larger carbon particles. After swelling by water, the ionomer layer absorbs water at the 17 wt% level. By changing the H2O/D2O ratio, it was further confirmed that the catalyst with the ionomer exhibits water repellence, whereas the bare catalyst without the ionomer is wetted by water. Because it is very difficult to extract more information, for instance regarding the Pt–Nafion interactions, by means of small-angle scattering, reflectometry and grazing-incidence scattering experiments with neutrons should be attempted on a model catalyst prepared on a flat substrate.
Heating of the cathode with a conical tip by atmospheric-pressure arc plasma
Authors: Liao Meng-Ran , Chen Tang , Lv Wei-Jian
Published: July 2019

Purpose

In this study, the authors performed a numerical investigation on the heating of a hot cathode with a conical tip by atmospheric arc, taking into account of the two temperature sheath effect for the first time.

Design/methodology/approach

The Schottky effect at cathode surface is considered, which is based on the analytic solution of a one-dimensional sheath model. The unified model allows one to predict the cathode-plasma heat transfer.

Findings

The total heat flux to cathode surface is smaller than its components’ heat flux due to electron back diffusion is as large as that due to ion flux with the increase of cathode length the total heat transported to the cathode body has an obvious decrease.

Originality/value

It is found that two kinds of solution exist for the cathode with a 140° conical tip; however, only one stable solution exists when the conical angle is reduced to 130°.
Lubricant compatibility of FKM seals in synthetic oils
Authors: Bulut Dilek , Krups Tatjana , Poll Gerhard , Giese Ulrich
Published: July 2019

Purpose

Elastomer seals are used in many applications. They are exposed to lubricants and additives at elevated temperatures, as well as mechanical stresses. They can only provide good sealing function when they have resistance to those factors. There are many elastomer-lubricant compatibility tests based on DIN ISO 1817 in industry. However, they are insufficient and costly. Correlations between the tests and the applications are inadequate. The purpose of this study is investigating lubricant compatibility of fluoroelastomers (FKM) seals in polyethylene-glycol (PG)- and polyalphaolefin (PAO)- based synthetic oils and developing a methodology to predict seal service life.

Design/methodology/approach

A new compatibility test which is more sufficient in terms of time and cost was developed and compared with a standard test, currently used in industry. Compatibility of FKM radial lip seals with PG- and PAO-based synthetic oils with different additives was investigated chemically and dynamically. Failure mechanisms were examined.

Findings

The new method and the Freudenberg Flender Test FB 73 11 008 showed similar results concerning damages and similar tendencies regarding wear. The additive imidazole derivative was the most critical. Static tests give indications of possible chemically active additives, but alone they are insufficient to simulate the dynamic applications.

Originality/value

The paper describes a new method to investigate elastomer-lubricant compatibility and gives first results with a variety of lubricants.
Preload effects on the static characteristics of three-lobe journal bearings lubricated with a couple stress fluid
Authors: Chetti Boualem , Crosby Wael Ahmed
Published: July 2019

Purpose

The purpose of this paper is to present the effect of the preload on the static characteristics of three-lobe bearings lubricated with a fluid blended with high polymer additives modeled as a couple stress fluid.

Design/methodology/approach

Based on the micro-continuum theory, the modified Reynolds equation for couple stress fluids is solved using a finite difference method to obtain the distribution of the pressure, the load-carrying capacity, the attitude angle, the friction coefficient and the side leakage for various values of the couple stress parameter and the preload factor.

Findings

The results show that the presence of a couple stress in the lubricants improves the static characteristics of this type of bearing compared to those lubricated with Newtonian fluids for any value of the preload factor. Thus, it is found that the preload significantly affects the performance of the three-lobe journal bearing lubricated with a couple stress fluid or a Newtonian fluid. Moreover, the investigation showed that increasing the preload factor exhibits an increase in the load carrying capacity and the attitude angle, but it decreases the friction coefficient and the side leakage especially at a lower preload factor. Furthermore, using a couple stress fluid and a higher preload factor led to a significant rise in the load carrying capacity and a significant reduction in the friction coefficient.

Practical implications

This study helped improve the performance characteristics of the three-lobe journal bearing.

Originality/value

The presence of couple stress in the lubricants improves the static characteristics of this type of bearing compared to those lubricated with Newtonian fluids for any value of the preload factor. The usage of the couple stress fluid and the higher preload factor led to a significant rise in the load carrying capacity and a significant reduction in the friction coefficient.
Consumer response to negative celebrity publicity: the effects of moral reasoning strategies and fan identification
Authors: Wang Sai , Kim Ki Joon
Published: July 2019

Purpose

In the context of celebrity endorsement, this study aims to demonstrate that the ways in which consumers adopt moral reasoning strategies (i.e. rationalization, decoupling and coupling) are largely dependent on the severity (i.e. high vs low) of celebrity transgressions and the degree to which they personally identify with the celebrity.

Design/methodology/approach

A between-subjects online experiment (N = 144) with two conditions, representing high- and low-severity celebrity transgressions, was conducted. Participants’ attitudes toward the celebrity and endorsed brand, their purchase intention for the endorsed product and the degrees to which they identified with the celebrity and adopted the three types of moral reasoning strategies were assessed.

Findings

The rationalization and decoupling strategies mediate the effects of highly negative information about a celebrity on consumer attitudes toward the celebrity and endorsed brand as well as on purchase intention for the endorsed product. In addition, consumers who identify strongly as fans of the celebrity in question are more likely to activate rationalization and decoupling strategies to process and evaluate transgressive behaviors than those with weaker fan identification.

Originality/value

By exploring the ways in which moral reasoning and fan identification work in processing negative information, this study provides insights into the psychological process through which negative news coverage of a celebrity endorser influences consumer attitudes and purchase intention.
Hygro-thermally induced stress intensity factor of an edge crack piezo laminated composite plate
Authors: Lal Achchhe , Jain Khushbu
Published: July 2019

Purpose

The purpose of this paper is to evaluate hygro-thermo-mechanically induced normalized stress intensity factor (NSIF) of an edge crack symmetric angle-ply piezo laminated composite plate (PLCP) using displacement correlation method.

Design/methodology/approach

In the present work, the governing equations are solved through conventional finite element method combined with higher order shear deformation plate theory utilizing the micromechanical approach.

Findings

The effects of crack length, the thickness of the plate and piezoelectric layer, stacking sequences, fiber volume fraction, position of piezoelectric layer, change in moisture and temperature, and voltage on the NSIF are examined. The numerical results are presented in the form of a table for the better understanding and accuracy. The present outlined approach is validated with results available in the literature. These results can become a benchmark for future studies.

Research limitations/implications

The mathematical models theoretically have been developed by considering different parameters. The results are generated using MATLAB 2015 software developed by the authors’ side.

Originality/value

The fracture analysis of a single edge crack PLCP with the effect of a piezoelectric layer at the different location of cracked structures, plate thickness, and actuator voltage and hygro-thermo loading is the novelty of research for health monitoring and high-performance analysis.
Trait sensitivities to seagrass fragmentation across spatial scales shape benthic community structure
Authors: Yeager Lauren A. , Geyer Julie K. , Fodrie Fredrick Joel
Published: July 2019

The structure of local ecological communities is thought to be determined by a series of hierarchical abiotic and biotic filters which select for or against species based on their traits. Many human impacts, like fragmentation, serve to alter environmental conditions across a range of spatial scales and may impact trait–environment interactions.

We examined the effects of environmental variation associated with habitat fragmentation of seagrass habitat measured from microhabitat to landscape scales in controlling the taxonomic and trait‐based community structure of benthic fauna.

We measured patterns in species abundance and biomass of seagrass epifauna and infauna sampled using sediment cores from 86 sites (across 21 meadows) in Back Sound, North Carolina, USA. We related local faunal community structure to environmental variation measured at three spatial scales (microhabitat, patch and landscape). Additionally, we tested the value of species traits in predicting species‐specific responses to habitat fragmentation across scales.

While univariate measures of faunal communities (i.e. total density, biomass and species richness) were positively related to microhabitat‐scale seagrass biomass only, overall community structure was predicted by environmental variation at the microhabitat, patch (i.e. patch size) and landscape (i.e. number of patches, landscape seagrass area) scales. Furthermore, fourth‐corner analysis revealed that species traits explained as much variation in organismal densities as species identity. For example, species with planktonic‐dispersing larvae and deposit‐feeding trophic modes were more abundant in contiguous, high seagrass cover landscapes while suspension feeders favoured more fragmented landscapes.

We present quantitative evidence supporting hierarchal models of community assembly which predict that interactions between species traits and environmental variation across scales ultimately drive local community composition. Variable responses of individual traits to multiple environmental variables suggest that community assembly processes that act on species via traits related to dispersal, mobility and trophic mode will be altered under habitat fragmentation. Additionally, with increasing global temperatures, the tropical seagrass Halodule wrightii is predicted to replace the temperate Zostera marina as the dominate seagrass in our study region, therefore potentially favouring species with planktonic‐dispersing larva and weakening the strength of environmental control on community assembly.
Th17 cells in glaucoma patients promote Ig production in IL‐17A and IL‐21‐dependent manner
Authors: Ren Yongbo , Qi Yanxiu , Su Xingjie
Published: July 2019

Elevated expression of autoantibodies is a hallmark of immune dysregulation in glaucoma and may cause retinal ganglion cell apoptosis and immune‐mediated nerve damage, thus contributing to the development of blindness. The cause of autoantibody upregulation remains unclear. Th17 cells are shown to promote autoimmunity and Ig production. Here, we demonstrate that the serum levels of interleukin (IL)‐17A and IL‐21 are comparable between glaucoma patients and non‐glaucoma controls. However, the levels of Th17‐promoting cytokines, such as tumour necrosis factor (TNF) IL‐6, are higher in glaucoma patients than in controls. Subsequently, we demonstrate that glaucoma patients present upregulated levels of Th17 cells that are quiescent directly ex vivo. Interestingly, compared to the Th17 cells from non‐glaucoma subjects, the Th17 cells from glaucoma patients present similar IL‐17A production capacity but significantly higher IL‐21 production capacity. Given that IL‐21 is also described as a specific cytokine of follicular helper T cells, the Ig production by B cells following co‐incubation with circulating Th17 cells is investigated. Th17 cells from glaucoma patients present significantly enhanced potential to promote Ig production than the Th17 cells from controls. Both glaucoma patient Th17 cells and control Th17 cells require IL‐17A and IL‐21 for Ig production. Overall, results from this study suggest that Th17 cells from glaucoma patients present elevated capacity to stimulate Ig production.
Oral delivery of pancreatitis‐associated protein by Lactococcus lactis displays protective effects in dinitro‐benzenesulfonic‐acid‐induced colitis model and is able to modulate the composition of the microbiota
Authors: Breyner Natalia M. , Vilas Boas Priscilla Bagano , Fernandes Gabriel , de Carvalho Rodrigo D. , Rochat Tatiana , Michel Marie‐Laure , Chain Florian , Sokol Harry , de Azevedo Marcela , Myioshi Anderson , Azevedo Vasco A. , Langella Philippe , Bermúdez‐Humarán Luis G. , Chatel Jean‐Marc
Published: July 2019

Antimicrobial peptides secreted by intestinal immune and epithelial cells are important effectors of innate immunity. They play an essential role in the maintenance of intestinal homeostasis by limiting microbial epithelium interactions and preventing unnecessary microbe‐driven inflammation. Pancreatitis‐associated protein (PAP) belongs to Regenerating islet‐derived III proteins family and is a C‐type (Ca+2 dependent) lectin. PAP protein plays a protective effect presenting anti‐inflammatory properties able to reduce the severity of colitis, preserving gut barrier and epithelial inflammation. Here, we sought to determine whether PAP delivered at intestinal lumen by recombinant Lactococcus lactis strain (LL‐PAP) before and after chemically induced colitis is able to reduce the severity in two models of colitis. After construction and characterization of our recombinant strains, we tested their effects in dinitro‐benzenesulfonic‐acid (DNBS) and Dextran sulfate sodium (DSS) colitis model. After the DNBS challenge, mice treated with LL‐PAP presented less severe colitis compared with PBS and LL‐empty‐treated mice groups. After the DSS challenge, no protective effects of LL‐PAP could be detected. We determined that after 5 days administration, LL‐PAP increase butyrate producer's bacteria, especially Eubacterium plexicaudatum. Based on our findings, we hypothesize that a treatment with LL‐PAP shifts the microbiota preventing the severity of colon inflammation in DNBS colitis model. These protective roles of LL‐PAP in DNBS colitis model might be through intestinal microbiota modulation.