bluuebunny/crossref_metadata_2025 huggingface dataset:
Stable Zn isotopes reveal the uptake and toxicity of zinc oxide engineered nanomaterials inPhragmites australis
Authors: Caldelas C , Poitrasson F , Viers J , Araus JL
Published: April 2020

The uptake, transport, and toxicity mechanisms of zinc oxide (ZnO) engineered nanomaterials (ZnO-ENMs) in aquatic plants remain obscure. We investigated ZnO-ENM uptake and phytotoxicity inPhragmites australisby combining Zn stable isotopes and microanalysis. Plants were exposed to four ZnO materials: micron-size ZnO, nanoparticles (NPs) of <100 nm or <50 nm, and nanowires of 50 nm diameter at concentrations of 0-1000 mg l−1. All ZnO materials reduced growth, chlorophyll content, photosynthetic efficiency, and transpiration and led to Zn precipitation outside the plasma membranes of root cells. Nanoparticles <50 nm released more Zn2+and were more toxic, thus causing greater Zn precipitation and accumulation in the roots and reducing Zn isotopic fractionation during Zn uptake. However, fractionation by the shoots was similar for all treatments and was consistent with Zn2+being the main form transported to the shoots. Stable Zn isotopes are useful to trace ZnO-ENM uptake and toxicity in plants.

Environmental Significance Statement

Our understanding of zinc oxide nanomaterials interaction with wetland plants is hampered by the lack of scientific consensus about their uptake and toxicity mechanisms in these species. This is a serious concern given the alarming global increase in the discharge of these nanomaterials into the environment and the key ecological roles of wetland plants. The Zn isotopic signature of plant tissue integrates all the Zn metabolic pathway throughout the plant’s life, giving insight about the form of Zn taken up, even if this later transforms into another Zn species. Thus, our findings clarify the exposure routes and the mechanisms of action of zinc oxide engineered nanomaterials in wetland plants while advancing the toolbox for plant physiology and environmental studies.

Table of contents

The Zn stable isotope composition of plants demonstrates that ZnO engineered nanomaterials dissolve before their uptake and accumulation by the roots (brightest inclusions in root cortex above).
Reversed sex-biased mutation rates for indels and base substitutions inDrosophila melanogaster
Authors: Törmä Lauri , Burny Claire , Schlötterer Christian
Published: April 2020

Sex biases in mutation rates may affect the rate of adaptive evolution. In many species, males have higher mutation rates than females when single nucleotide variants (SNVs) are considered. In contrast, indel mutations in humans and chimpanzees are female-biased. InDrosophila melanogaster, direct estimates of mutation rates did not uncover sex differences, but a recent analysis suggested the presence of male-biased SNVs mutations. Here we study the sex-specific mutation processes using mutation accumulation data from mismatch-repair deficientD. melanogaster. We find that sex differences in flies are similar to the ones observed in humans: a higher mutation rate for SNVs in males and a higher indel rate in females. These results have major implications for the study of neutral variation and adaptation inDrosophila.
Runs of homozygosity in killer whale genomes provide a global record of demographic histories
Authors: Hooper Rebecca , Excoffier Laurent , Forney Karin A. , Gilbert M. Thomas P. , Martin Michael D. , Morin Phillip A. , Wolf Jochen B.W. , Foote Andrew D.
Published: April 2020

Runs of homozygosity (ROH) occur when offspring receive the same ancestral haplotype from both parents, and, accordingly, reduce individual heterozygosity. Their distribution throughout the genome contains information on the probability of inbreeding mediated by mating system and population demography. Here, we investigate variation in killer whale demographic history as reflected in genome-wide heterozygosity, using a global dataset of 26 genomes. We find an overall pattern of lower heterozygosity in genomes sampled at high latitudes, with hundreds of short ROH (< 1Mbp) reflecting high background relatedness due to coalescence of haplotypes during bottlenecks associated with founder events during post-glacial range expansions. Across most of the species’ range, intermediate length ROH (1-10Mb) revealed long-term inbreeding in 22 of the 26 sampled killer whale genomes, consistent with the high social philopatry observed in all populations studied to date. Inbreeding coefficients (FROH) were comparable to those reported in other taxa with long-term low population size, such as bonobos and the Native American Karitiana of the Brazilian Amazon. The extreme outlier in this dataset, a Scottish killer whale, was homozygous over one-third of the autosomes (41.6%) with a distinct distribution of ROH length, indicating generations of inbreeding. This exceeds autozygosity in emblematic examples of long-term inbreeding, such as the Altai Neanderthal, and eastern lowland and mountain gorillas. The fate of this Scottish killer whale population, in which no calves have been born in over two decades, may be inextricably linked to its demographic history and consequential inbreeding depression.
Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts
Authors: Zaghlool Ammar , Niazi Adnan , Björklund Åsa K. , Westholm Jakub Orzechowski , Ameur Adam , Feuk Lars
Published: April 2020

Transcriptome analysis has mainly relied on analyzing RNA sequencing data from whole cells, overlooking the impact of subcellular RNA localization and its influence on our understanding of gene function, and interpretation of gene expression signatures in cells. Here, we performed a comprehensive analysis of cytosolic and nuclear transcriptomes in human fetal and adult brain samples. We show significant differences in RNA expression for protein-coding and lncRNA genes between cytosol and nucleus. Transcripts displaying differential subcellular localization belong to particular functional categories and display tissue-specific localization patterns. We also show that transcripts encoding the nuclear-encoded mitochondrial proteins are significantly enriched in the cytosol compared to the rest of protein-coding genes. Further investigation of the use of the cytosolic or the nuclear transcriptome for differential gene expression analysis indicates important differences in results depending on the cellular compartment. These differences were manifested at the level of transcript types and the number of differentially expressed genes. Our data provide a resource of RNA subcellular localization in the human brain and highlight differences in using the cytosolic or the nuclear transcriptomes for differential expression analysis.
Intravenous sulforhodamine B reduces alveolar surface tension, improves oxygenation and reduces ventilation injury in a respiratory distress model
Authors: Wu You , Ngyuen Tam L. , Perlman Carrie E.
Published: April 2020

In the neonatal (NRDS) and acute (ARDS) respiratory distress syndromes, mechanical ventilation supports gas exchange but can cause ventilation-induced lung injury (VILI) that contributes to high mortality. Further, surface tension,T, should be elevated and VILI is proportional toT. Surfactant therapy is effective in NRDS but not ARDS. Sulforhodamine B (SRB) is a potential alternativeT-lowering therapeutic. In anesthetized male rats, we injure the lungs with 15 min of 42 ml/kg tidal volume,VT, and zero end-expiratory pressure ventilation. Then, over 4 hrs, we support the rats with protective ventilation –VTof 6 ml/kg with positive end-expiratory pressure. At the start of the support period, we administer intravenous non-T-altering fluorescein (targeting 27 μM in plasma) without or with therapeutic SRB (10 nM). Throughout the support period, we increase inspired oxygen fraction, as necessary, to maintain >90% arterial oxygen saturation. At the end of the support period we sacrifice the rat; sample systemic venous blood for injury marker ELISAs; excise the lungs; combine confocal microscopy and servo-nulling pressure measurement to determineT in situin the lungs; image fluorescein in alveolar liquid to assess local permeability; and determine lavage protein content and wet-to-dry ratio (W/D), both to assess global permeability. Lungs exhibit focal injury. Surface tension is elevated 72% throughout control lungs and in uninjured regions of SRB-treated lungs, but normal in injured regions of treated lungs. Sulforhodamine B administration improves oxygenation, reduces W/D and reduces plasma injury markers. Intravenous SRB holds promise as a therapy for respiratory distress.

New and Noteworthy

Sulforhodmaine B lowersT. Given the problematic intratracheal delivery of surfactant therapy for ARDS, intravenous SRB might constitute an alternative therapeutic. In a lung injury model, we find that intravenously administered SRB crosses the injured alveolar-capillary barrier, reducesTspecifically in injured lung regions, improves oxygenation and reduces the degree of further lung injury. Intravenous SRB administration might help respiratory distress patients, including those with the novel coronavirus, avoid mechanical ventilation or, once ventilated, survive.
Molecular investigations on a chimeric strain ofStaphylococcus aureussequence type 80
Authors: Gawlik Darius , Ruppelt-Lorz Antje , Müller Elke , Reißig Annett , Hotzel Helmut , Braun Sascha D. , Söderquist Bo , Ziegler-Cordts Albrecht , Ehricht Ralf , Monecke Stefan
Published: April 2020

An Eritrean patient was admitted with suspected tuberculous cervical lymphadenitis. While no mycobacteria were detected in pus from this process, culture yielded PVL-positive, methicillin-susceptibleStaphylococcus aureus. Microarray hybridisation assigned the isolate to clonal complex (CC) 80 but revealed unusual features, including the presence of the ORF-CM14 enterotoxin homologue and of an ACME-III element as well as the absence ofetDandedinB.The isolate was subjected to both, Illumina and Nanopore sequencing allowing characterisation of deviating regions within the strain’s genome. Atypical features of this strain were attributable to the presence of two genomic regions that originated from otherS. aureuslineages and that comprised, respectively, 3% and 1.4% of the genome. One deviating region extended fromwalJtosirB. It comprised ORF-CM14 and the ACME-III element. A homologous, but larger fragment was also found in an atypicalS. aureusCC1/ST567 strain whose lineage might have served as donor of this genomic region. This region itself is a chimera comprising fragments from CC1 as well as fragments of unknown origin. The other region of another 3% of the genome comprised the region fromhtsBtoecfA2. It was very similar to CC1 sequences. This suggests either an incorporation of CC1 DNA into the study strain, or it might alternatively suggest a recombination event affecting “canonical” CC80. As the study strain bears witness of several recombination events, such complex and large-scale events cannot be rare and exceptional, despite a mainly clonal nature ofS. aureus. Although the exact mechanism is not yet clear, chimerism seems to be an additional pathway in the evolution ofS. aureus, possibly being responsible for the transmission also of virulence and resistance factors. An organism that can shuffle, swap or exchange major parts of its genome by a yet unknown mechanism would have an evolutionary advantage compared to a strictly clonal organism.
Organic manure managements increases soil microbial community structure and diversity in double-cropping paddy field of Southern China
Authors: Tang Haiming , Xiao Xiaoping , Li Chao , Pan Xiaochen , Cheng Kaikai , Shi Lihong , Wang Ke , Li Weiyan
Published: April 2020

The soil physicochemical properties were affected by different fertilizer managements, and the soil microbial communities were changed. Fertilizer regimes were closely relative to the soil texture and nutrient status in a double-cropping paddy field of southern China. However, there was limited information about the influence of different long-term fertilizer management practices on the soil microbial communities in a double-cropping rice (Oryza sativaL.) fields. Therefore, the 39-year long-term fertilizer regimes on soil bacterial and fungal diversity in a double-cropping paddy field of southern China were studied by using Illumina sequencing and quantitative PCR technology in the present paper. The filed experiment were including chemical fertilizer alone (MF), rice straw residue and chemical fertilizer (RF), 30% organic manure and 70% chemical fertilizer (OM), and without fertilizer input as a control (CK). The results showed that diversity indices of soil microbial communities with application of organic manure and rice straw residue treatments were higher than that without fertilizer input treatment. Application of organic manure and rice straw residue managements increase soil bacterial abundance of the phylumProteobacteria, Actinobacteria, andGammaproteobacteria, and soil fungi abundance of the phylumBasidiomycota, ZygomycotaandTremellaleswere also increased. Compared with CK treatment, the value of Richness, Shannon and McIntosh indices, and taxonomic diversity were increased with RF and OM treatments. This finding demonstrated that RF and OM treatments modify soil bacterial and fungal diversity. Therefore, the combined application of organic manure or rice straw residue with chemical fertilizer managements could significantly increase the abundance of profitable functional bacteria and fungi species in double-cropping rice fields of southern China.
Conservation genetics of regionally extinct peregrine falcons (Falco peregrinus) and unassisted recovery without genetic bottleneck in southern England
Authors: Weaving Angela , Jackson Hazel A. , Nicholls Michael K. , Franklin Jon , Vega Rodrigo
Published: April 2020

The peregrine falcon (Falco peregrinus) has been affected by persecution, pollution, trade and habitat degradation, but it is considered a flagship conservation success story because of successful reintroductions. However, in the UK there were never formal reintroduction programmes for peregrine falcons, and it appears that UK populations – and specifically the Sussex peregrines of the English south coast – recently recovered from a population crash unassisted. To study this, we obtained samples from contemporary populations in southern England, Ireland, continental Europe, domestic-bred peregrine falcons, and from England pre-population crash. Using microsatellite and mtDNA control region data, the genetic diversity and structure, signatures of genetic bottlenecks, and potential origin of the Sussex peregrines was investigated. We found low levels of genetic diversity across all peregrine falcon populations, low but significant genetic differentiation among all populations, and a few private alleles, indicating some level of genetic structure in European peregrines. Although we could not pinpoint the origin of the Sussex peregrines, the data suggests that it is not likely to have originated from escaped domestic birds or from adjacent European populations. The results obtained here parallel other studies on peregrines elsewhere showing low genetic diversity but genetic structure. We conclude that not enough time elapsed for genetic erosion to occur due to the population bottleneck, and that at least for the Sussex peregrines there is no need for genetic conservation by wild-take and subsequent captive breeding programmes as long as current protection measures remain in place.
D4: Deep Drug-drug interaction Discovery and Demystification
Authors: Noor Adeeb , Liu-Wei Wang , Barnawi Ahmed , Nour Redhwan , Assiri Abdullah A , Chan Bukhari Syed Ahmad , Hoehndorf Robert
Published: April 2020

Motivation

Drug-drug interactions (DDIs) are complex processes which may depend on many clinical and non-clinical factors. Identifying and distinguishing ways in which drugs interact remains a challenge. To minimize DDIs and to personalize treatment based on accurate stratification of patients, it is crucial that mechanisms of interaction can be identified. Most DDIs are a consequence of metabolic mechanisms of interaction, but DDIs with different mechanisms occur less frequently and are therefore more difficult to identify.

Results

We developed a method (D4) for computationally identifying potential DDIs and determining whether they interact based on one of eleven mechanisms of interaction. D4 predicts DDIs and their mechanisms through features that are generated through a deep learning approach from phenotypic and functional knowledge about drugs, their side-effects and targets. Our findings indicate that our method is able to identify known DDIs with high accuracy and that D4 can determine mechanisms of interaction. We also identify numerous novel and potential DDIs for each mechanism of interaction and evaluate our predictions using DDIs from adverse event reporting systems.

Availability

https://github.com/bio-ontology-research-group/D4

Contact

arnoor@kau.edu.sa and robert.hoehndorf@kaust.edu.sa
Exploring the interaction between the pupillary light response after exogenous attentional cueing and detection performance
Authors: Wagenvoort Tiemen J. , Timmerman Rosanne H. , Van der Stigchel Stefan , Fabius Jasper
Published: April 2020

Pupil size changes under different light conditions. Whereas this pupillary light response (PLR) has long been regarded to be influenced by luminance only, recent studies indicated the PLR is also modulated by cognitive factors such as the allocation of spatial attention. This attentional modulation of the PLR has previously been hypothesized to facilitate detection and discrimination of visual information. Here, we replicated the finding that the pupil dilates when a cue is presented at the dark side of a screen and constricts when the cue is presented at the bright side, even when the eyes are fixated at the center. Furthermore, we investigated whether this modulation of the PLR, evoked by exogenous shifts of covert attention, facilitates perception operationalized as detection performance for threshold stimuli. Results showed that a larger pupil was indeed related to increased detection performance, although this effect was restricted to conditions in which both cue and target appeared on a dark surface. Our findings are in line with the notion that pupil dilations improve detectability, whereas pupil constrictions enhance discriminability of small stimuli.
Geographic mosaic of selection by avian predators on hindwing warning colour in a polymorphic aposematic moth
Authors: Ronka Katja , Valkonen Janne , Nokelainen Ossi , Rojas Bibiana , Gordon Swanne , Burdfield-Steel Emily , Mappes Johanna
Published: April 2020

Warning signals are predicted to develop signal monomorphism via positive frequency-dependent selection (+FDS) albeit many aposematic systems exhibit signal polymorphism. To understand this mismatch, we conducted a large-scale predation experiment in four locations, among which the frequencies of hindwing warning coloration of aposematicArctia plantaginisdiffer. Here we show that selection by avian predators on warning colour is predicted by local morph frequency and predator community composition. We found +FDS to be strongest in monomorphic Scotland, and in contrast, lowest in polymorphic Finland, where different predators favour different male morphs. +FDS was also found in Georgia, where the predator community was the least diverse, whereas in the most diverse avian community in Estonia, hardly any models were attacked. Our results support the idea that spatial variation in predator and prey communities alters the strength or direction of selection on warning signals, thus facilitating a geographic mosaic of selection.
Metabolic differences between symbiont subpopulations in the deep-sea tubewormRiftia pachyptila
Authors: Hinzke Tjorven , Kleiner Manuel , Meister Mareike , Schlüter Rabea , Hentschker Christian , Pané-Farré Jan , Hildebrandt Petra , Felbeck Horst , Sievert Stefan M. , Bonn Florian , Völker Uwe , Becher Dörte , Schweder Thomas , Markert Stephanie
Published: April 2020

The hydrothermal vent tube wormRiftia pachyptilalives in intimate symbiosis with intracellular sulfur-oxidizing gammaproteobacteria. Although the symbiont population consists of a single 16S rRNA phylotype, bacteria in the same host animal exhibit a remarkable degree of metabolic diversity: They simultaneously utilize two carbon fixation pathways and various energy sources and electron acceptors. Whether these multiple metabolic routes are employed in the same symbiont cells, or rather in distinct symbiont subpopulations, was unclear. AsRiftiasymbionts vary considerably in cell size and shape, we enriched individual symbiont cell sizes by density gradient centrifugation in order to test whether symbiont cells of different sizes show different metabolic profiles. Metaproteomic analysis and statistical evaluation using clustering and random forests, supported by microscopy and flow cytometry, strongly suggest thatRiftiasymbiont cells of different sizes represent metabolically dissimilar stages of a physiological differentiation process: Small symbionts actively divide and may establish cellular symbiont-host interaction, as indicated by highest abundance of the cell division key protein FtsZ and highly abundant chaperones and porins in this initial phase. Large symbionts, on the other hand, apparently do not divide, but still replicate DNA, leading to DNA endoreduplication. Highest abundance of enzymes for CO2fixation, carbon storage and biosynthesis in large symbionts indicates that in this late differentiation stage the symbiont’s metabolism is efficiently geared towards the production of organic material. We propose that this division of labor between smaller and larger symbionts benefits the productivity of the symbiosis as a whole.
Poly (ADP-ribose) induces α-synuclein aggregation in neuronal-like cells and interacts with phosphorylated α-synuclein in post mortem PD samples
Authors: Puentes Laura N. , Lengyel-Zhand Zsofia , Lee Ji Youn , Hsieh Chia-Ju , Schneider Mark E. , Edwards Kimberly J. , Luk Kelvin C. , Lee Virginia M.-Y. , Trojanowski John Q. , Mach Robert H.
Published: April 2020

Background

Poly (ADP-ribose) (PAR) is a negatively charged polymer that is biosynthesized by Poly (ADP-ribose) Polymerase-1 (PARP-1) and regulates various cellular processes. Alpha-synuclein (αSyn) is an intrinsically disordered protein (IDP) that has been directly implicated with driving the onset and progression of Parkinson’s disease (PD). The mechanisms by which αSyn elicits its neurotoxic effects remain unclear. Recent findings indicate that one of the key processes driving PD pathology are oligomeric species of αSyn. Furthermore, it is well established that the main components of Lewy bodies (LBs) and Lewy neurites (LNs) in PD patients are aggregated hyperphosphorylated (S129) forms of αSyn (pαSyn).

Methods

We used biochemical and immunofluorescence-based assays to explore if PARP-1 enzymatic product (PAR) drives the conversion of monomeric αSyn into aggregated assemblies. We performed quantitative measurements using in situ proximity ligation assays (PLA) on a transgenic murine model of α-synucleinopathy (M83-SNCA*A53T) and post-mortem PD/PDD patient samples to characterize PAR-pαSyn interactions. Additionally, we used bioinformatic approaches and site-directed mutagenesis to identify PAR-binding regions on fibrillar αSyn.

Results

Our studies show that elevated intracellular levels of PAR promote the transition of αSyn into higher molecular weight forms. We report that PAR-pαSyn interactions are predominant in pathological states. Moreover, we confirm that the interactions between PAR and αSyn involve electrostatic forces between negatively charged PAR and lysine residues on the N-terminal region of αSyn.

Conclusions

PAR plays a critical role in the early stages of monomeric αSyn aggregation, thereby attributing to PD pathogenesis. Based on our results, we report that PAR seeds monomeric αSyn aggregation and directly interacts with phosphorylated αSyn in conditions that are pathologically relevant to PD.
Improved genetically encoded near-infrared fluorescent calcium ion indicators forin vivoimaging
Authors: Qian Yong , Cosio Danielle M. Orozco , Piatkevich Kiryl D. , Aufmkolk Sarah , Su Wan-Chi , Celiker Orhan T. , Schohl Anne , Murdock Mitchell H. , Aggarwal Abhi , Chang Yu-Fen , Wiseman Paul W. , Ruthazer Edward S. , Boyden Edward S. , Campbell Robert E.
Published: April 2020

Near-infrared (NIR) genetically-encoded calcium ion (Ca2+) indicators (GECIs) can provide advantages over visible wavelength fluorescent GECIs in terms of reduced phototoxicity, minimal spectral cross-talk with visible-light excitable optogenetic tools and fluorescent probes, and decreased scattering and absorption in mammalian tissues. Our previously reported NIR GECI, NIR-GECO1, has these advantages but also has several disadvantages including lower brightness and limited fluorescence response compared to state-of-the-art visible wavelength GECIs, when used for imaging of neuronal activity. Here, we report two improved NIR GECI variants, designated NIR-GECO2 and NIR-GECO2G, derived from NIR-GECO1. We characterized the performance of the new NIR GECIs in cultured cells, acute mouse brain slices, andC. elegansandXenopus laevis in vivo. Our results demonstrate that NIR-GECO2 and NIR-GECO2G provide substantial improvements over NIR-GECO1 for imaging of neuronal Ca2+dynamics.
Viral cross-linking and solid-phase purification enables discovery of ribonucleoprotein complexes on incoming RNA virus genomes
Authors: Kim Byungil , Arcos Sarah , Rothamel Katherine , Ascano Manuel
Published: April 2020

The initial interactions between incoming, pre-replicated RNA virus genomes and host protein factors are important in infection and immunity. Yet there are no current methods to study these crucial events. We established VIR-CLASP (VIRal Cross-Linking And Solid-phase Purification) to identify the primary viral RNA-host protein interactions. First, host cells are infected with 4SU-labeled RNA viruses and irradiated with 365 nm light to crosslink 4SU-labeled viral genomes and interacting proteins from host or virus. The cross-linked RBPs are purified by solid-phase reversible immobilization (SPRI) beads with protein denaturing buffers, and then identified by proteomics. With VIR-CLASP, only the incoming viral genomes are labeled with 4SU, so cross-linking events specifically occur between proteins and pre-replicated viral genomic RNA. Since solid-phase purification under protein-denaturing conditions is used to pull-down total RNA and cross-linked RBPs, this facilitates investigation of potentially all RNA viruses, regardless of RNA sequence. Preparation of 4SU-labeled virus takes ∼7 days and VIR-CLASP takes 1 day.
3D Variability Analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM
Authors: Punjani Ali , Fleet David J.
Published: April 2020

Single particle cryo-EM excels in determining static structures of protein molecules, but existing 3D reconstruction methods have been ineffective in modelling flexible proteins. We introduce 3D variability analysis (3DVA), an algorithm that fits a linear subspace model of conformational change to cryo-EM data at high resolution. 3DVA enables the resolution and visualization of detailed molecular motions of both large and small proteins, revealing new biological insight from single particle cryo-EM data. Experimental results demonstrate the ability of 3DVA to resolve multiple flexible motions ofα-helices in the sub-50 kDa transmembrane domain of a GPCR complex, bending modes of a sodium ion channel, five types of symmetric and symmetry-breaking flexibility in a proteasome, large motions in a spliceosome complex, and discrete conformational states of a ribosome assembly. 3DVA is implemented in thecryoSPARCsoftware package.
Widespread imprinting of transposable elements and young genes in the maize endosperm
Authors: Anderson Sarah N , Zhou Peng , Higgins Kaitlin , Brandvain Yaniv , Springer Nathan M
Published: April 2020

Fertilization and seed development is a critical time in the plant life cycle, and coordinated development of the embryo and endosperm are required to produce a viable seed. In the endosperm, some genes show imprinted expression where transcripts are derived primarily from one parental genome. Imprinted gene expression has been observed across many flowering plant species, though only a small proportion of genes are imprinted. Understanding the rate of turnover for gain or loss of imprinted expression has been complicated by the reliance on single nucleotide polymorphisms between alleles to enable testing for imprinting. Here, we develop a method to use whole genome assemblies of multiple genotypes to assess for imprinting of both shared and variable portions of the genome using data from reciprocal crosses. This reveals widespread maternal expression of genes and transposable elements with presence-absence variation within maize and across species. Most maternally expressed features are expressed primarily in the endosperm, suggesting that maternal de-repression in the central cell facilitates expression. Furthermore, maternally expressed TEs are enriched for maternal expression of the nearest gene. Read alignments over maternal TE-gene pairs indicate fused transcripts, suggesting that variable TEs contribute imprinted expression of nearby genes.
Structural features of an infectious recombinant PrPScprion using solid state NMR
Authors: Martín-Pastor Manuel , Codeseira Yaiza B. , Spagnolli Giovanni , Eraña Hasier , Fernández Leticia C. , Bravo Susana , Iglesias Alba , López-Moreno Rafael , Veiga Sonia , Biasini Emiliano , Sánchez-Pedregal Víctor M. , Castilla Joaquín , Requena Jesús R.
Published: April 2020

PrPSc, the first described and most notorious prion, is the only protein known to cause epidemics of deadly disease. Its properties are encoded in its unique structure. Here we report a first solid state NMR study of a uniformly labelled (U-13C,15N)-Bank vole (BV) infectious recombinant PrPScprion. C-C, C-H and N-H spectra were obtained with MAS rotation of the sample at up to 60 kHz. We obtained amino acid-type secondary structure information and used it to challenge a physically plausible atomistic model of PrPScconsisting of a 4-rung β solenoid recently proposed by us. In all cases, our model was compatible with the data. This study shows that elucidation of the structure of PrPScis within reach using recombinant PrPSc, NMR, and our model as a guiding tool.
β-alanine or L-carnosine prevents the development of pale, soft and exudative pork by inhibiting the glycolysis of porcinelongissimus dorsimuscle
Authors: Zhao Lihong , Chen Peng , Li Wenxiang , Li Lan , Liu Yaojun , Zhang Jianyun , Ji Cheng , Ma Qiugang
Published: April 2020

Carnosine plays an important role in regulating muscle buffering capacity and glycolysis. In order to investigate the effects of dietaryβ-alanine, L-histidine, and L-carnosine supplementation on the pH value, glycolytic potential, the activities of AMP-activated protein kinase (AMPK) and pyruvate kinase (PK) activities in the porcinelongissimus dorsimuscle, a total of 60 barrows with an average body weight (BW) of 50.5 ± 1.7 kg were assigned into five groups which received diets containing basal diet (control, CON), 0.04%β-alanine (β-ALA), 0.06% L-histidine (L-HIS), 0.04%β-alanine+0.06% L-histidine (β-ALA+L-HIS), or 0.1% L-carnosine (L-CAR). The results showed that dietary supplementation of the combination ofβ-ALA and L-HIS or L-CAR significantly increased (P< 0.05) the average daily gain (ADG) of pigs with 50-75 kg BW, compared with other three groups. Compared with L-CAR group, L-HIS supplementation significantly decreased (P< 0.05) the average daily feed intake (ADFI) of pigs. There were no significant difference (P> 0.05) in back fat thickness and loin eye area among treatments. At 0, 1 and 24 h postmortem (PM) the pH values in thelongissimus dorsimuscle (LM) of pigs receiving L-CAR were higher (P< 0.05) than that of pigs receiving CON diet. The redness (a*) values of LM of pigs in theβ-ALA+L-HIS or L-CAR group were higher (P< 0.05) than those in other three groups. The glycolytic potential of LM was not significantly different (P> 0.05) among treatments. At 1, 24 h PM the AMPK activities in LM of pigs receivingβ-ALA,β-ALA+L-HIS and L-CAR were much lower (P< 0.05) than those of pigs receiving CON diet or L-HIS. 0.1% L-carnosine or 0.04%β-alanine supplemented to pigs’ diet was effective in regulating AMPK and PK activities in the porcinelongissimus dorsimuscle and preventing the development of pale, soft and exudative (PSE) pork.
TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data
Authors: Jha Kunal Kumar , Gruza Barbara , Kumar Prashant , Chodkiewicz Michal Leszek , Dominiak Paulina Maria
Published: April 2020

Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X—H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X—H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (d
min ≤ 0.83 Å) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.
Communicative action and supportive behaviors for environmental CSR practices: an attitude-based segmentation approach
Authors: Li Jo-Yun , Overton Holly , Bhalla Nandini
Published: April 2020

Purpose

While the segmentation approach has been frequently employed to explore individuals' environment-friendly behaviors, the investigation of environmental corporate social responsibility (CSR) communication by using such a method is limited. Given that the importance of the role of public segmentation is well documented in both public relations and environmental management literatures, the present study attempts to fill the gap by exploring whether consumers can be segmented on the basis of attitudinal factors, and, if so, how this segmentation informs communication efforts aimed at promoting companies' environmental CSR programs.

Design/methodology/approach

This segmentation approach is examined based on a survey of 470 participants. Results of a k-means cluster analysis identified three subgroups: active publics, aware publics and latent publics.

Findings

Survey results provide empirical support evidence on how different public segmentation approaches can be used to predict individual communication behaviors on environmental CSR issues. Segmentation approach that considered individuals' attitudes on environmental issues and their perceptions on company environmental CSR practices helps identify three subgroups. Significant differences regarding communicative action and supporting behaviors among the three groups are identified and discussed.

Originality/value

This study provides key insights about public segmentation and different publics' communicative action, and supportive behaviors provide direction for future research investigations that will strengthen theoretical arguments and best practices in public relations.
Analysis of a novel two-lane lattice model with consideration of density integral and relative flow information
Authors: Qi Xinyue , Cheng Rongjun , Ge Hongxia
Published: April 2020

Purpose

This study aims to consider the influence of density difference integral and relative flow difference on traffic flow, a novel two-lane lattice hydrodynamic model is proposed. The stability criterion for the new model is obtained through the linear analysis method.

Design/methodology/approach

The modified Korteweg de Vries (KdV) (mKdV) equation is derived to describe the characteristic of traffic jams near the critical point. Numerical simulations are carried out to explore how density difference integral and relative flow difference influence traffic stability. Numerical and analytical results demonstrate that traffic congestions can be effectively relieved considering density difference integral and relative flow difference.

Findings

The traffic congestions can be effectively relieved considering density difference integral and relative flow difference.

Originality/value

Novel two-lane lattice hydrodynamic model is presented considering density difference integral and relative flow difference. Applying the linear stability theory, the new model’s linear stability is obtained. Through nonlinear analysis, the mKdV equation is derived. Numerical results demonstrate that the traffic flow stability can be efficiently improved by the effect of density difference integral and relative flow difference.
Perils of conversation: #MeToo and opportunities for peacebuilding
Authors: Ross Nancy , Bookchin Sue
Published: April 2020

Purpose

The purpose of this paper is to discuss the opportunities for future organizational and leadership research presented by positioning dialogue related to the #MeToo movement within a peacebuilding agenda. The #MeToo movement raised public consciousness about the pervasiveness of sexual assault and harassment in schools, workplaces and other institutions by an international social media campaign. However, subsequent discussions are often charged with hostility and outrage that result in divisiveness within workplaces and other settings that can further silence about these issues. The authors argue a community peacebuilding framework can create space to have difficult conversations to further the efforts of the #MeToo movement.

Design/methodology/approach

The authors will discuss the implications of a peacebuilding framework by the discussion of a case study in a rural setting to highlight the ways in which community conversations necessary to further the goals of the #MeToo movement.

Findings

A grassroots community peacebuilding framework can present opportunities for victims, offenders, family members and the community to voice expressions harms experienced and to enable processes of accountability. Promotion of a positive relational peace includes opportunities for education, skill development and conflict resolution that are healing and transformative for individuals and communities.

Research limitations/implications

The systemic social and cultural change required to prevent sexual harassment and sexual assault must happen within face-to-face relationships within community dialogue.

Practical implications

The authors argue a critical relational peace lens offers an emancipatory framework that can initiate change from the bottom up to facilitate social healing and further the efforts of the #MeToo movement.

Social implications

Grassroots peacebuilding invites a relational peace established by dialogue within communities. This dialogue is often not easy but is recognized as essential to establishing trust, resolving conflict and fostering community integrity.

Originality/value

In this paper, the authors offer a community peacebuilding framework to provide skill development and a vision necessary to host difficult conversations to inform the next wave of the #MeToo movement.
Combined framing effects on attitudes and behavioral intentions toward mortgage advertisements
Authors: Dobson David S. , Poels Karolien
Published: April 2020

Purpose

Mortgage lenders often combine a variety of framing strategies when developing mortgage advertisements. To date, these frames have mostly been studied separately. This paper, however, studies the combined framing effects of message valence, specificity, and temporality on consumers' mortgage decision-making.

Design/methodology/approach

A mixed methods design was used. First, 13 unique print ads collected from a Canadian newspaper were analyzed for content. Second, a 2 × 2 × 2 scenario-based experiment with 400 undergraduate participants examined the framing effects of valence, specificity and temporality on attitudes toward the mortgage advertising message, the product advertised, and the brand, as well as on consumers' behavioral intentions toward the advertised mortgage product.

Findings

The content analysis suggests that combined framing does exist in print ads. A positive message with a fixed term and a specific interest rate were the most commonly used frames. The experiment revealed that, for behavioral intentions, the main effect of the message temporality was significant. The effects of advertising a long-term mortgage on behavioral intentions were more favorable than those of advertising a short-term mortgage.

Practical implications

This research provides a combined framing model for designing advertising strategies for the financial services industry to market complex financial products, such as mortgage loans to consumers. This is relevant to lenders when designing a persuasive package or ads for potential customers.

Originality/value

This study is the first of its kind to investigate the effects of combinations of message frames on consumers' mortgage decision-making, while also advancing the understanding of message framing theory for the financial services industry.
Prioritizing determinants of effective whistle blowing (WB)
Authors: Niazi Abdul Aziz Khan , Qazi Tehmina Fiaz , Ali Irfan , Ahmad Rashid
Published: April 2020

Purpose

In current vista of corporate governance (CG), whistleblowing (WB) has become critical for practitioners, researchers and other stakeholders. This study aims to identify, prioritize and analyze the interrelationships of determinants of effective WB on the basis of opinion of a medium-sized panel of experts.

Design/methodology/approach

It is a cross-sectional descriptive study conducted in the field setting. A self-administered structured questionnaire was used to collect primary data from the respondents. This study follows an interpretive structural modeling (ISM) approach.

Findings

This study found that the factor “specific law for WB” has maximum driving power but minimum dependence and occupies bottom level (the most critical level) in the ISM model. The Matrice d’Impacts Croisés Multiplication Appliquée á un Classement analysis revealed that there is no autonomous and dependent factor in the model. There are eight linking factors and only one independent factor.

Research limitations/implications

The study found that the factor “specific law for WB” has maximum driving power but minimum dependence and occupies bottom level (the most critical level) in the ISM model. The Matrice d'Impacts Croisés Multiplication Appliquée á un Classement analysis revealed that there is no autonomous and no clear-cut dependent factor in the model. There are eight linking factors out of which five have high dependence as well, and there is only one independent factor.

Practical implications

This study has ensued in identification of significant challenging issues in WB and in development of interrelationships to gain insights into priority of these issues. This study uses limited primary data in context of Pakistan; therefore, generalizability of the findings is limited.

Originality/value

This study presents a novel theoretical and conceptual model focused on effective WB. The value of the study on effective WB is highly relevant for today’s complex organizations but incipient in literature. The insights provided by the study have vital importance for corporations to embark on the regime of reforms in CG.
The effectiveness of multiple brand portfolios: the role of directional dominance and brand interference on brand evaluation
Authors: Won June , Lee J. Lucy
Published: April 2020

Purpose

The purposes of the study were (1) to examine whether directional dominance between co-existing athlete brands and sponsor brands exists; (2) to explore whether directional dominance influences consumers' memory interference; and (3) to test whether brand interference interacts with directional dominance among brands to influence consumer evaluation and behaviors under multiple endorsement and sponsorship portfolios.

Design/methodology/approach

The research is a 3 (directional dominance: symmetric dominance vs. asymmetric dominance with existing vs. asymmetric dominance with newly endorsed brand) x 2 (brand memory interference: interference vs. no interference) between-subjects factorial design.

Findings

The results indicate that (1) directional dominance influenced consumer brand interference, and directional dominance interacted with brand interference on (2) brand evaluation and (3) purchase intention in multiple brand portfolios.

Originality/value

Considering that conventional single-sponsor sponsorship or single-endorser endorsement portfolios are increasingly rare, research on concurrent circumstances of multiple endorsers and multiple endorsed brands in multiple brand portfolios was necessary. By expanding and reconceptualizing the context of brand networks, this study provides empirical evidence on how the dominance and directionality between endorser and (existing and newly) endorsed brands—an athlete endorser's strong pre-existing association with an existing endorsed brand in particular—influenced consumer brand interference and the brand evaluation in multiple brand portfolios.
Women and politics: a case study of political empowerment of Indian women
Authors: Sharma Eliza
Published: April 2020

Purpose

This paper aims to identify the dimensions of the political empowerment of Indian women and assess the factors responsible for the lacunas that hold women back in their potential.

Design/methodology/approach

The research was based on primary data collected through a personal interview method from a sample of 68 women managers working in five different sectors of the Indian economy, namely; IT, education, telecom, banking, and hospitality sector. Further, data on the five factors from a sample of 423 women employees from the above-mentioned sectors have been collected and analyzed using a multiple regression model with control variables (marital status and generation gap).

Findings

The major factors churned out that are needed for the political empowerment of women are namely, information or awareness, family support or family environment, legal environment, political environment, and personal ambitions or internal motivation.

Originality/value

The present study has presented new insight into the field of women and politics by providing a case study into the dimensions of political empowerment among Indian women. The pilot model developed in this study can be initiated and replicated across the land on being successful.