bluuebunny/crossref_metadata_2025 huggingface dataset:
HIV-1 drug resistance profiling using amino acid sequence space cartography
Authors: Pikalyova Karina , Orlov Alexey , Lin Arkadii , Tarasova Olga , Marcou Gilles , Horvath Dragos , Poroikov Vladimir , Varnek Alexandre
Published: August 2021

Human immunodeficiency virus (HIV) drug resistance is a global healthcare issue. The emergence of drug resistance demands treatment adaptation. Computational methods predicting the drug resistance profile from genomic data of HIV isolates are advantageous for monitoring drug resistance in patients. Yet, the currently existing computational methods for drug resistance prediction are either not suitable for complex mutational patterns in emerging HIV strains or lack interpretability of prediction results which is of paramount importance in clinical practice. Hence, to overcome these limitations, new approaches for the HIV drug resistance prediction combining high accuracy and interpretability are required. In this work, a new methodology for the analysis of protein sequence data based on the application of generative topographic mapping was developed and applied for HIV drug resistance profiling. It allowed achieving high accuracy of resistance predictions and intuitive interpretation of prediction results. The developed approach was successfully applied for the prediction of HIV resistance towards protease, reverse-transcriptase and integrase inhibitors and in-depth analysis of HIV resistance-inducing mutation patterns. Hence, it can serve as an efficient and interpretable tool to suggest optimal treatment regimens.
Zona Incerta activity dynamics underlying associative fear learning and fear generalization
Authors: Li Zhuoliang , Rizzi Giorgio , Tan Kelly R.
Published: August 2021

Recent studies suggest that the Zona Incerta (ZI) plays a role in fear learning and recall. However, there is a clear gap in knowledge as to whether the ZI can encode fear evoking threats and cues that predict them. Here, we subject mice to a classical fear conditioning paradigm while recording the in-vivo calcium dynamics of ZI neurons. We observed that ZI neurons can encode not only a fear evoking stimulus, but can also learn to encode predictive cues, associate them with the unconditioned fear evoking stimulus, and discriminate them from neutral non-predictive cues. While the ZI across all mice learned to become mainly excited by fear predictive cues, only mice that did not generalize fear became largely inhibited by non-predictive cues and better discriminated the two. Together, we provide extensive evidence that the ZI differentially encode fear predictive and non-predictive cues in a generalization dependent manner.
piRNAs of Caenorhabditis elegans broadly silence nonself sequences through functionally random targeting
Authors: McEnany John , Meir Yigal , Wingreen Ned
Published: August 2021

Small non-coding RNAs such as piRNAs serve as guides for Argonaute proteins, enabling sequence-specific, post-transcriptional regulation of gene expression. The piRNAs of Caenorhabditis elegans have been observed to bind targets with high mismatch tolerance, and appear to lack specific transposon targets, unlike piRNAs in Drosophila melanogaster and other organisms. These observations support a model in which C. elegans piRNAs provide a broad, indiscriminate net of silencing, acting in competition with siRNAs associated with the CSR-1 Argonaute that specifically protect self genes from silencing. However, the breadth of piRNA targeting has not been subject to in-depth quantitative analysis, nor has it been explained how piRNAs are distributed across sequence space to achieve complete coverage. Through a bioinformatic analysis of piRNA sequences, incorporating an original metric of piRNA-target distance, we demonstrate that C. elegans piRNAs are functionally random, in that their coverage of sequence space is comparable to that of random sequences. By possessing a sufficient number of distinct, essentially random piRNAs, C. elegans is able to target arbitrary nonself sequences with high probability. This result elucidates the mechanism by which newly transcribed mRNAs in C. elegans are classified as self or nonself, and has implications for piRNA evolution and biogenesis.
Water soluble, red emitting, carbon nanoparticles stimulate 3D cell invasion via clathrin-mediated endocytic uptake
Authors: Singh Udisha , Teja Aditya Guduru , Walia Shanka , Vaswani Payal , Dalvi Sameer , Bhatia Dhiraj
Published: August 2021

Bright, fluorescent nanoparticles with excitation and emission towards the red end of the spectrum are highly desirable in the field of bioimaging. We present here a new class of organic carbon-based nanoparticles (CNPs) with robust quantum yield and fluorescence towards the red region of the spectrum. Using organic substrates like para-phenylenediamine (PPDA) dispersed in diphenyl ether and reflux conditions, we achieved scalable amounts of CNPs of the average size of 25 nm. These CNPs were readily uptaken by different mammalian cells, and we show that they prefer clathrin-mediated endocytosis for their cellular entry route. Not only can these CNPs be specifically uptaken in cells, but they also stimulate cellular processes like cell invasion from 3D spheroid models. These new class of CNPs, which have sizes similar to proteinaceous ligands, hold immense potential for their surface functionalization, whereby they could be explored as promising bioimaging agents for biomedical imaging and intracellular drug delivery.
Label-free monitoring of 3D cortical neuronal growth in vitro using optical diffraction tomography
Authors: Lee Ariel J. , Yoon DongJo , Han SeungYun , Hugonnet Herve , Park WeiSun , Park Je-Kyun , Nam YoonKey , Park YongKeun
Published: August 2021

The highly complex central nervous systems of mammals are often studied using three-dimensional (3D) in vitro primary neuronal cultures. A coupled confocal microscopy and immunofluorescence labeling are widely utilized for visualizing the 3D structures of neurons. However, this requires fixation of the neurons and is not suitable for monitoring an identical sample at multiple time points. Thus, we propose a label-free monitoring method for 3D neuronal growth based on refractive index tomograms obtained by optical diffraction tomography. The 3D morphology of the neurons was clearly visualized, and the developmental processes of neurite outgrowth in 3D spaces were analyzed for individual neurons.

Abstract Figure
Genomic analyses of human adenoviruses unravel novel recombinant genotypes associated with severe infections in pediatric patients
Authors: Akello Joyce Odeke , Kamgang Richard , Barbani Maria Teresa , Suter-Riniker Franziska , Aebi Christoph , Beuret Christian , Paris Daniel H. , Leib Stephen L , Ramette Alban
Published: August 2021

Background

Human Adenoviruses (HAdVs) are highly contagious pathogens of clinical importance, especially among the pediatric population. Studies on comparative viral genomic analysis of cases associated with severe and mild infections due to HAdV are limited. Using whole-genome sequencing (WGS), we investigated whether there were any differences between circulating HAdV strains associated with severe infections (meningitis, sepsis, convulsion, sudden infant death syndrome, death, and hospitalization) and mild clinical presentations in pediatric patients hospitalized between the years 1998 and 2017 in a tertiary care hospital group in Bern, Switzerland covering a population base of approx. 2 million inhabitants. The HAdV species implicated in causing severe infections in this study included HAdV species C genotypes (HAdV1, HAdV2, and HAdV5). Clustering of the HAdV whole-genome sequences of the severe and mild cases did not show any differences except for one sample (isolated from a patient presenting with sepsis, meningitis, and hospitalization) that formed its own cluster with HAdV species C genotypes. This isolate showed intertypic recombination events involving four genotypes, had the highest homology to HAdV89 at complete genome level, but possessed the fiber gene of HAdV1, thereby representing a novel genotype of HAdV species C. The incidence of potential recombination events was higher in severe cases than in mild cases. Our findings confirm that recombination among HAdVs is important for molecular evolution and emergence of new strains. Therefore, further research on HAdVs, particularly among susceptible groups, is needed and continuous surveillance is required for public health preparedness including outbreak investigations.
Coilin oligomerization and remodeling by Nopp140 reveals a hybrid assembly mechanism for Cajal bodies
Authors: Courchaine Edward , Machyna Martin , Straube Korinna , Sauyet Sarah , Enright Jade , Neugebauer Karla M.
Published: August 2021

Cajal bodies (CBs) are ubiquitous nuclear membraneless organelles (MLOs) that promote efficient biogenesis of RNA-protein complexes. Depletion of the CB scaffolding protein coilin is lethal for vertebrate embryogenesis, making CBs a strong model for understanding the structure and function of MLOs. Although it is assumed that CBs form through biomolecular condensation, the biochemical and biophysical principles that govern CB dynamics have eluded study. Here, we identify features of the coilin protein that drive CB assembly and shape. Focusing on coilin’s N-terminal domain (NTD), we discovered its unexpected capacity for oligomerization in vivo. Single amino acid mutational analysis of coilin revealed distinct molecular interactions required for oligomerization and binding to the Nopp140 ligand, which facilitates CB assembly. We demonstrate that the intrinsically disordered regions of Nopp140 have substantial condensation properties and suggest that Nopp140 binding thereby remodels stable coilin oligomers to form a particle that recruits other functional components.
Large differences in carbohydrate degradation and transport potential in the genomes of lichen fungal symbionts
Authors: Resl Philipp , Bujold Adina R. , Tagirdzhanova Gulnara , Meidl Peter , Rallo Sandra Freire , Kono Mieko , Fernández-Brime Samantha , Guðmundsson Hörður , Andrésson Ólafur Sigmar , Muggia Lucia , Mayrhofer Helmut , McCutcheon John P. , Wedin Mats , Werth Silke , Willis Lisa M. , Spribille Toby
Published: August 2021

Lichen symbioses are generally thought to be stabilized by the transfer of fixed carbon compounds from a photosynthesizing unicellular symbiont to a fungus. In other fungal symbioses, carbohydrate subsidies correlate with genomic reductions in the number of genes for plant cell wall-degrading enzymes (PCWDEs), but whether this is the case with lichen fungal symbionts (LFSs) is unknown. We predicted genes encoding carbohydrate-active enzymes (CAZymes) and sugar transporters in 17 existing and 29 newly sequenced genomes from across the class Lecanoromycetes, the largest extant clade of LFSs. Despite possessing lower mean numbers of PCWDE genes compared to non-symbiont Ascomycota, all LFS genomes possessed a robust suite of predicted PCWDEs. The largest CAZyme gene numbers, on par with model species such as Penicillium, were retained in genomes from the subclass Ostropomycetidae, which are found in crust lichens with highly specific ecologies. The lowest numbers were in the subclass Lecanoromycetidae, which are symbionts of many generalist macrolichens. Our results suggest that association with phototroph symbionts does not in itself result in functional loss of PCWDEs and that PCWDE losses may have been driven by adaptive processes within the evolution of specific LFS lineages. The inferred capability of some LFSs to access a wide range of carbohydrates suggests that some lichen symbioses may augment fixed CO2 with carbon from external sources.

Significance

Lichen symbioses are considered self-contained autotrophic systems in which the total carbon economy is the sum of phototroph-fixed CO2, supplied to a fungus as sugars. In other fungal-plant symbioses, such as mycorrhizae, plant-derived sugar subsidies are associated with loss of plant cell wall-degrading enzymes (PCWDEs). We compared PCWDE inventories in 46 genomes from the largest group of lichen fungal symbionts (LFSs) with non-symbionts from across Ascomycota. We found that despite lower overall gene numbers, all LFSs retain PCWDEs, and some possess gene numbers and functional diversity on par with non-symbionts. Our results suggest that association with a phototroph does not necessarily result in PCWDE loss, and some lichens may obtain carbon from sources other than CO2 fixation.
Regulatory perturbations of ribosome allocation reshape the growth proteome with a trade-off in adaptation capacity
Authors: Hidalgo David , Martínez-Ortiz César A. , Palsson Bernhard O. , Jiménez José I. , Utrilla José
Published: August 2021

Bacteria regulate their cellular resource allocation to enable fast growth-adaptation to a variety of environmental niches. We studied the ribosomal allocation, growth and expression profiles of two sets of fast-growing mutants of Escherichia coli K-12 MG1655 in glucose minimal medium. Mutants with only 3 of the seven copies of ribosomal RNA operons grew faster than the wild-type strain in minimal media and show similar phenotype to previously studied rpoB mutants. Higher growth rates due to increased ribosome content affected resource allocation. Expression profiles of fast-growing mutants shared downregulation of hedging functions and upregulated growth functions. Mutants showed longer diauxic shifts and reduced activity of gluconeogenic promoters during glucose-acetate shifts, suggesting reduced availability of the RNA Polymerase for expressing hedging proteome. These results show that the regulation of ribosomal allocation underlies the growth/hedging phenotypes obtained from laboratory evolution experiments. We show how two different regulatory perturbations (rRNA promoters or rpoB mutations) reshape the proteome for growth with a concomitant fitness cost

Highlights

Mutants with only 3 ribosomal operons grow faster than wild-type in minimal medium

Δ4 rrn and rpoB mutants share phenotypic traits

Faster growth of mutants is achieved by increased ribosome content

Fast-growing mutants display reduced hedging expression and adaptation trade-offs

Despite similar ribosomal content in rich medium the mutants present growth defects
Repurposing brewery contaminant yeast as production strains for low-alcohol beer fermentation
Authors: Krogerus Kristoffer , Eerikäinen Ronja , Aisala Heikki , Gibson Brian
Published: August 2021

A number of fungal isolates were recently obtained from a survey of the microbiota of multiple breweries and brewery products. Here, we sought to explore whether any of these brewery contaminants could be repurposed for beneficial use in beer fermentations, with particular focus on low-alcohol beer. 56 yeast strains were first screened for the utilization of different carbon sources, ability to ferment brewer’s wort, and formation of desirable aroma compounds. A number of strains appeared maltose-negative and produced desirable aromas without obvious off-flavours. These were selected for further scaled-up wort fermentations. The selected strains efficiently reduced wort aldehydes during fermentation, thus eliminating undesirable wort-like off-flavours, and produced a diverse volatile aroma profile. Sensory analysis of the beer samples using projective mapping identified two strains,Trigonopsis cantarelliiandCandida sojae, that produced beers similar to a commercial reference lager beer. 30 L-scale wort fermentations were performed with these two strains together with a commercialSaccharomycodes ludwigiireference strain. Both strains performed comparably to the commercial reference, and theT. cantarelliistrain in particular, produced low amounts of off-flavours and a significantly higher amount of the desirable monoterpene alcoholtrans-geraniol. The strain was also sensitive to common food preservatives and antifungal compounds, and unable to grow at 37 °C, suggesting it is relatively easily controllable in the brewery, and appears to have low risk of pathogenicity. This study shows how the natural brewery microbiota can be exploited as a source of non-conventional yeasts for low-alcohol beer production.

Take Away

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Fungal isolates from brewery microbiota were screened for beer production

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Numerous maltose-negative strains were tested for low-alcohol beer fermentation

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Trigonopsis cantarelliishowed promise compared to a commercial reference strain

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T. cantarelliiproduced no off-flavours and higher levels oftrans-geraniol
A comparative study of population genetic structure reveals patterns consistent with selection at functional microsatellites in common sunflower
Authors: Ranathunge Chathurani , Chimahusky Melody , Welch Mark E
Published: August 2021

Microsatellites have long been considered non-functional, neutrally evolving regions of the genome. Recent findings suggest that they can function as drivers of rapid adaptive evolution. Previous work on common sunflower identified 479 transcribed microsatellites where allele length significantly correlates with gene expression (eSTRs) in a stepwise manner. Here, a population genetic approach is used to test whether eSTR allele length variation is under selection. Genotypic variation among and within populations at 13 eSTRs was compared with that at 19 anonymous microsatellites in 672 individuals from 17 natural populations of sunflower from across a cline running from Saskatchewan to Oklahoma. Expected heterozygosity, allelic richness, and allelic diversity were significantly lower at eSTRs, a pattern consistent with higher relative rates of purifying selection. Further, an analysis of variation in microsatellite allele lengths (lnRV), and heterozygosities (lnRH), indicate recent selective sweeps at the eSTRs. Mean microsatellite allele lengths at four eSTRs within populations are significantly correlated with latitude consistent with the predictions of the tuning knob model which predicts stepwise relationships between microsatellite allele length and phenotypes. This finding suggests that shorter or longer alleles at eSTRs may be favored in climatic extremes. Collectively, our results imply that eSTRs are likely under selection and that they may be playing a role in facilitating local adaptation across a well-defined cline in the common sunflower.
An abundant myeloid progenitor shapes neonatal hematopoiesis of naked mole-rats
Authors: Emmrich Stephan , Trapp Alexandre , Seluanov Andrei , Gorbunova Vera
Published: August 2021

The naked mole-rat became an attractive model for biomedical research due to its exceptional longevity and resistance to disease, yet the developmental properties of naked mole-rat stem and progenitor compartments are poorly understood. Here we report a high frequency bone marrow progenitor, which we termed TC90, exclusively present in neonatal animals. TC90s were marked by an immunophenotype resembling adult naked mole-rat common myeloid progenitors (CMP) with mature neutrophilic Thy1.1-antigen levels and showed a clear differentiation bias and transcriptome signature towards myelopoiesis. TC90s overexpressed both CXCL12 and its alternative receptor CXCR7, thereby abrogating their homing capacity and produced multiple secreted matrix components related to neonatal bone marrow niche formation. We hypothesize that the TC90 cell population protects newborns during the critical transition at birth and shortly beyond by boosting a supply of innate immune cells. In summary, our results identify a transient cell stage during postnatal hematopoiesis unique to naked mole-rats.
Genome-wide protein-DNA interaction site mapping using a double strand DNA-specific cytosine deaminase
Authors: Gallagher Larry A. , Velazquez Elena , Brook Peterson S. , Charity James C. , Hsu FoSheng , Radey Matthew C. , Gebhardt Michael J. , de Moraes Marcos H. , Penewit Kelsi M. , Kim Jennifer , Andrade Pia A. , LaFramboise Thomas , Salipante Stephen J. , de Lorenzo Victor , Wiggins Paul A. , Dove Simon L. , Mougous Joseph D.
Published: August 2021

DNA–protein interactions (DPIs) are central to such fundamental cellular processes as transcription and chromosome maintenance and organization. The spatiotemporal dynamics of these interactions dictate their functional consequences; therefore, there is great interest in facile methods for defining the sites of DPI within cells. Here, we present a general method for mapping DPI sites in vivo using the double stranded DNA-specific cytosine deaminase toxin DddA. Our approach, which we term DddA-sequencing (3D-seq), entails generating a translational fusion of DddA to a DNA binding protein of interest, inactivating uracil DNA glycosylase, modulating DddA activity via its natural inhibitor protein, and DNA sequencing for genome-wide DPI detection. We successfully applied this method to three Pseudomonas aeruginosa transcription factors that represent divergent protein families and bind variable numbers of chromosomal locations. 3D-seq offers several advantages over existing technologies including ease of implementation and the possibility to measure DPIs at single-cell resolution.
MVsim: a toolset for quantifying and designing multivalent interactions
Authors: Bruncsics Bence , Errington Wesley J. , Sarkar Casim A.
Published: August 2021

Arising through multiple binding elements, multivalency can specify the avidity, duration, cooperativity, and selectivity of biomolecular interactions, but quantitative prediction and design of these properties has remained challenging. Here we present MVsim, an application suite built around a configurational network model of multivalency to facilitate the quantification, design, and mechanistic evaluation of multivalent binding phenomena through a simple graphical user interface. To demonstrate the utility and versatility of MVsim, we first show that both monospecific and multispecific multivalent ligand-receptor interactions, with their noncanonical binding kinetics, can be accurately simulated. We then quantitatively predict the ultrasensitivity and performance of multivalent-encoded protein logic gates, evaluate the inherent programmability of multispecificity for selective receptor targeting, and extract rate constants of conformational switching for the SARS-CoV-2 spike protein and model its binding to ACE2 as well as multivalent inhibitors of this interaction. MVsim is freely available at https://sarkarlab.github.io/MVsim/.
Multidirectional measures of shear modulus in skeletal muscle
Authors: Reyna William E. , Perreault Eric J. , Ludvig Daniel
Published: August 2021

The material properties of muscle play a central role in how muscle resists joint motion, transmits forces internally, and repairs itself. While many studies have evaluated muscle’s tensile material properties, few have investigated muscle’s shear properties. None of which have taken into account muscle’s anisotropic structure or investigated how different muscle architecture affect muscle’s shear properties. The objective of this study was to quantify the shear moduli of skeletal muscle in three orientations relevant to the function of whole muscle. We collected data from the extensor digitorum longus, tibialis anterior, and soleus harvested from both hindlimbs of 12 rats. These muscles were chosen to further evaluate the consistency of shear moduli across muscles with different architectures. We calculated the shear modulus in three orientations: parallel, perpendicular, and across with respect to muscle fiber alignment; while the muscle was subjected to increasing shear strain. For all muscles and orientations, the shear modulus increased with increasing strain. The shear modulus measured perpendicular to fibers was greater than in any other orientation. Despite architectural differences between muscles, we did not find a significant effect of muscle type on shear modulus. Our results show that in rat, muscles’ shear moduli vary with respect to fiber orientation and are not influenced by architectural differences in muscles.
Postnatal SETD1B is essential for learning and the regulation of neuronal plasticity genes
Authors: Michurina Alexandra , Sakib M Sadman , Kerimoglu Cemil , Krüger Dennis Manfred , Kaurani Lalit , Islam Md Rezaul , Devesh Joshi Parth , Schröder Sophie , Centeno Tonatiuh Pena , Zhou Jiayin , Pradhan Ranjit , Cha Julia , Xu Xingbo , Eichele Gregor , Zeisberg Elisabeth M. , Kranz Andrea , Stewart A. Francis , Fischer Andre
Published: August 2021

Histone 3 lysine 4 methylation (H3K4me) is mediated by six different lysine methyltransferases. Amongst these enzymes SET domain containing 1b (SETD1B) has been linked to syndromic intellectual disability but its role in the postnatal brain has not been studied yet. Here we employ mice that lackSetd1bfrom excitatory neurons of the postnatal forebrain and combine neuron-specific ChIP-seq and RNA-seq approaches to elucidate its role in neuronal gene expression. We observe that SETD1B controls the expression of genes with a broad H3K4me3 peak at their promoters that represent neuronal enriched genes linked to learning and memory function. Comparative analysis to corresponding data from conditionalKmt2aandKmt2bknockout mice suggests that this function is specific to SETD1B. Moreover, postnatal loss ofSetd1bleads to severe learning impairment, suggesting that SETD1B-mediated regulation of H3K4me levels in postnatal neurons is critical for cognitive function.
Integration of short- and long-term responses to environmental stimuli shape seasonal transcriptome dynamics
Authors: Kurita Yuko , Takimoto Hironori , Kamitani Mari , Hashida Yoichi , Kashima Makoto , Tezuka Ayumi , Tanabata Takanari , Nagano Atsushi J.
Published: August 2021

Plants must respond to various seasonally changing environmental stimuli. In a previous study, seasonally oscillating genes were identified by a massive time-series transcriptome analysis for the wild population ofArabidopsis hallerissp.gemmifera, a sister species toArabidopsis thaliana. It was not clear how environmental stimuli shaped the seasonal expression pattern of these seasonally oscillating genes. In this study we show that responses in different time-scales contributed to the formation of seasonal expression patterns for several genes. To analyze the seasonally oscillating genes, we established an experimental system to mimic seasonal expression trends usingA. thalianaand a “smart growth chamber mini,” a hand-made low-cost small chamber.Arabidopsis thalianaplants were cultured under conditions that mimicked the average monthly temperatures and daylengths under different day-scale incubation. In total, the seasonal trends of 1627 seasonally oscillating genes were mimicked, and they showed varying temporal responses (constant, transient, and incremental) to environmental stimuli. Our results suggest that plants perceive and integrate information regarding environmental stimuli in the field by combining seasonally oscillating genes with different temporal responsiveness.
Alternative oxidase1a and 1d limit proline-dependent oxidative stress and aid salinity recovery in Arabidopsis
Authors: Oh Glenda Guek Khim , O’Leary Brendan M. , Signorelli Santiago , Harvey Millar A.
Published: August 2021

A link between Pro catabolism and mitochondrial reactive oxygen species production has been established across eukaryotes and in plants increases in leaf respiration rates have been reported following Pro exposure. Here we investigated how alternative oxidases (AOXs) of the mitochondrial electron transport chain accommodate the large, atypical flux resulting from Pro catabolism and limit oxidative stress during Pro breakdown in mature Arabidopsis leaves. Following Pro treatment, AOX1a and AOX1d accumulate at transcript and protein levels, with AOX1d approaching the level of the typically dominant AOX1a isoform. We therefore sought to determine the function of both AOX isoforms under Pro respiring conditions. Oxygen consumption rate measurements in aox1a and aox1d leaves suggested these AOXs can functionally compensate for each other to establish enhanced AOX catalytic capacity in response to Pro. Generation of aox1a.aox1d lines showed complete loss of AOX proteins and activity upon Pro treatment, yet full respiratory induction in response to Pro remained possible via the cytochrome pathway. However, aox1a.aox1d leaves suffered increased levels of oxidative stress and damage during Pro metabolism compared to WT or the single mutants. During recovery from salt stress, when high rates of Pro catabolism occur naturally, photosynthetic rates in aox1a.aox1d recovered slower than WT or the single aox lines, showing that both AOX1a and AOX1d are beneficial for cellular metabolism during Pro drawdown following osmotic stress. This work provides physiological evidence of a beneficial role for AOX1a but also the less studied AOX1d isoform in allowing safe catabolism of alternative respiratory substrates like Pro.

One sentence summary

The alternative oxidase of plant mitochondria contributes to Pro catabolism by preventing oxidative stress in the electron transport chain and this aids recovery of leaf metabolic rates following salinity stress.
BMAL1 dephosphorylation determines the pace of the circadian clock
Authors: Schibler Ueli
Published: August 2021

In mammals, virtually all body cells harbor cell-autonomous and self-sustained circadian oscillators that rely on delayed negative feedback loops in gene expression. Transcriptional activation and repression play a major role in keeping these clocks ticking, but numerous post-translational mechanisms—and particularly the phosphorylation of core clock components by protein kinases—are also critically involved in setting the pace of these timekeepers. In this issue of Genes & Development, Klemz and colleagues (pp. 1161–1174) now show how dephosphorylation of BMAL1 by protein phosphatase 4 (PPP4) participates in the modulation of circadian timing.
Labeling the 5′ Termini of DNA with Bacteriophage T4 Polynucleotide Kinase
Authors: Green Michael R. , Sambrook Joseph
Published: August 2021

The removal of 5′ phosphates from nucleic acids with phosphatases and their readdition in radiolabeled form by bacteriophage T4 polynucleotide kinase is a widely used technique for generating 32P-labeled probes. When the reaction is performed efficiently, 40%–50% of the protruding 5′ termini in the reaction becomes radiolabeled. However, the specific activity of the resulting probes is not as high as that obtained by other radiolabeling methods because only one radioactive atom is introduced per DNA molecule. Nevertheless, the availability of [γ-32P]ATP with specific activities in the 3000–7000 Ci/mmol range allows the synthesis of probes suitable for many purposes. This protocol includes procedures for labeling the 5′ ends of dsDNA and oligonucleotides.
Teaching history in Japan and England: exchanging ideas and comparing knowledge
Authors: Fearns-Davies Matthew , Kubota Tsutomu , Tachibana Fumina , Kato Yuko , Davies Ian
Published: August 2021

Purpose

This paper describes and discusses collaboration between history teachers in England and Japan. The purpose of this paper is to explore the ways in which history is taught in each country as a part of a general commitment to international collaboration and as a means by which we could explore the connection between history education and global citizenship education.

Design/methodology/approach

The teachers created two lessons (one from England and one from Japan) about the Russian revolution. Both lessons were taught in each country. Data were gathered from students and teachers to aid reflections on the nature and outcome of the collaboration.

Findings

The collaboration was very positive. Teachers and students were excited to work together and to experience different ways of learning about the past. There were different approaches to the ways in which knowledge was characterized in each country (teachers in England emphasizing contextually based historical interpretations; teachers in Japan emphasizing content and contextual knowledge).

Originality/value

This work contributes to the limited amount of research that is currently available about professional collaboration between high school teachers and students of history in Japan and England. The arguments that are made about the opportunities for international collaboration in the context of different characterizations of pedagogical content knowledge contribute to a relatively unexplored field. The authors contribute to our understandings of the relationship between history education and global citizenship education.
Lived experiences of inequalities in the USA: a sense-making perspective
Authors: Khilji Shaista E.
Published: August 2021

Purpose

Inequality is an important organizational phenomenon. Scholars have argued that inequalities persistently dwell in the flow of our lives and have a lingering impact. Yet, despite such compelling evidence, research has overlooked how individuals make sense of the inequalities they face inside and outside the organizations. The purpose of this paper was to address these gaps and capture its complexity on individual lived experiences with inequalities.

Design/methodology/approach

The present study used Seidman's adapted 2-interview strategy to collect the data. The first interview placed the participant's life history at the center, allowing the participant to share their childhood and adulthood experiences with inequalities inside and outside the organizations. The second interview focused on the concrete details of the participant's present lived experience and their reflections on the meaning of their experiences. In total, the present study relied on 26 interviews with 13 participants.

Findings

Lived experiences provided an extended-time view and allowed the researcher to explore how study participants perceived, coped and were shaped by inequalities throughout their lives. In addition, the sense-making perspective offered a new lens to study inequalities. Findings underscore the racial, class and gendered dynamics within organizations supporting their intersectional impact and acknowledge the pre-existing societal norms that condition individual actions and choices.

Originality/value

The study presents an “engaged” view of inequality to highlight it as a cumulative and complex experience. The findings help us recognize that participants are immersed in their specific contexts to act, negotiate, empower and make decisions under real-life pressures. Overall, the study pushes the boundaries of inequality research beyond its current episodic treatment.
Building a digital marketing internship program for technology-based start-ups: an exploratory study of student experiences
Authors: Merz G. Russell , Ward Jamie , Qrunfleh Sufian , Gibson Bud
Published: August 2021

Purpose

The purpose of this paper is to describe the role and characteristics of the summer internship program (Digital Summer Clinic) delivered by Eastern Michigan University. The authors report the results of an exploratory study of interns participating in the Digital Summer Clinic over a five-year time period. The study captures and analyzes the experiences of interns as expressed in structured interviews and blog posts.

Design/methodology/approach

The study data were text from structured interviews and blog posts capturing the “voice” of the interns. A natural language processing (NLP) analysis of the text corpus, consisting of 43 interviews and blog posts, resulted in the identification of 242 unique stem-terms used by interns in describing the internship experiences. The authors used the JMP Pro 15.2 Text Explorer algorithm (It is defined as a suite of computer programs for statistical analysis developed by the JMP business unit of SAS Institute) to extract the terms that were subsequently transformed and analyzed with factor analysis and regression to address the research questions.

Findings

The factor analysis results found six dimensions or themes, defined by the stem-terms used by student interns, best described the internship experience. The authors then explored the relationship between the six themes and the umbrella term “internship” with multiple regression analysis. The regression findings suggest a hierarchy of effects with the theme “Introducing Professional Opportunities” being the theme most predictive of the umbrella term.

Originality/value

The methodology used within the paper is unique in several ways when compared to other research investigating internship programs. First, it uses NLP analysis for the qualitative analysis of text-based descriptions of student experiences over a five-year time horizon. Second, the data analysis uses transformed text to quantitatively determine the major dimensions or themes expressed by the interns about their experiences in the Summer Clinic program. Finally, the relative importance of the themes identified provided direction for future program development.
Entrepreneurship analysis in Spanish universities
Authors: Renart Vicens Gemma , Vall-llosera Casanovas Laura , Saurina Canals Carme , Serra Laura
Published: August 2021

Purpose

Entrepreneurship requires the attitudes and capabilities needed to begin new and innovative projects able to create positive impacts in the economy of a society. Given that it forms the basis from which new companies, products and innovations emerge, it is a very relevant term in business. With the aim of strengthening these capabilities, many universities are incorporating new educational strategies into their curricula to boost entrepreneurial intention and business skills among their students. This study aims to determine the factors that intervene in the entrepreneurial spirit of students in Spanish universities by examining areas of study, different personal and contextual characteristics, and the type of training students receive in entrepreneurship.

Design/methodology/approach

Data collected from 33,182 students in 77 Spanish universities in the 2018 edition of the Global University Entrepreneurial Spirit Students' Survey (GUESSS) is examined in an exhaustive univariate and bivariate descriptive and inferential analysis. Furthermore, the relationship between the entrepreneurial index and the different explicative variables is modelled, and a basic random effect for the area of study is introduced to detect differences at this level.

Findings

Economics, engineering and health sciences presented higher than average entrepreneurial indices. Regarding the type of training, only voluntary education in entrepreneurship influenced entrepreneurial spirit, albeit not equally in all areas of study.

Originality/value

This study’s results can help universities to incorporate new educational strategies into their curricula to boost entrepreneurial intention and business skills among students by focusing resources where they are most efficient.
Understanding sense of safety and trustworthiness of tourism information among migrant visitors
Authors: Preko Alexander , Gyepi-Garbrah Theophilus Francis
Published: August 2021

Purpose

The migration-tourism discourse has gained attention in global tourism and mobility among scholars because of the vast contributions of migrant visitors to various sectors of the host country's economy, including the tourism and hospitality industry. However, few studies appear to have been undertaken on the subject matter, particularly within the developing country tourism context. The purpose of this research was to assess and understand migrant visitors' sense of safety among five different nationalities (United Kingdom, USA, Germany, China and India) and their perceptions on trustworthiness of tourism information.

Design/methodology/approach

Anchored on the national cultural dimension of Hofstede model, this study sampled 306 migrant visitors, with the use of one-way analysis of variance (ANOVA) and the Games–Howell post-hoc test to examine mean differences of nationalities, with regard to trust of tourism information and sense of safety. Finally, the multiple regression analysis was conducted to establish the significant effects of national culture characteristics and trustworthiness of tourism information on sense of safety of migrant visitors.

Findings

The study finds that there were no significant differences in the sense of safety by the five nationalities. However, national culture characteristics (power distance and uncertainty avoidance) and trustworthiness of tourism information were significant predictors of sense of safety of migrant visitors.

Research limitations/implications

This research adopted only two cultural dimensions of the Hofstede's model, so future studies within the migration-tourism literature should consider adopting other cultural dimensions of the model.

Practical implications

The research provides, first, insight into sense of safety, trustworthiness of tourism information and national culture characteristics which are relevant for destination marketers, the ministry of tourism and local tourism officials to promote safety tourism.

Originality/value

The study expands the application of the cultural dimension of Hofstede model within the migration-tourism literature and establishes that national cultural characteristics and trustworthiness of tourism information are significant predictors of sense of safety of migrant visitors.
Hospitality and host–guest paradigm in China: a rejoinder to Chen
Authors: Qi Changlong
Published: August 2021

Purpose

This rejoinder aims to critique some of the perspectives in Chen’s (2018) study on hospitality and host–guest paradigm in China.

Design/methodology/approach

In this preliminary probe into Chen’s study, critical analysis is performed on Chen’s approaches, whereas document analysis is applied to the relevant ancient Chinese writings. Translations are the author’s own unless indicated otherwise.

Findings

Chen’s views are problematic and supported by patchy evidence. “Hierarchy principle” and “host-centric foundation” do not hold up. In a series of asymmetrical comparisons, Chen goes a bit too far in arguing for uniqueness.

Originality/value

This rejoinder presents valid critiques of Chen’s study, thus directing future research in the right direction. It is of some significance to clarify Chen’s misrepresentations and offer a truer and fuller account of Chinese hospitality, given the difficulty for international scholars to validate Chen’s views because of language barrier and cultural unfamiliarity.
Strategic planning in higher education: a simplified B-VAR model
Authors: Williams Densil A.
Published: August 2021

Purpose

Executives who are engaged in strategic planning for higher education generally complain about the process and the lack of clear outcomes from the strategic plan. They generally argue that the process is complex and sometimes confusing and the end result does not justify the time spent in preparing the plan. The extant literature on strategic planning in higher educational institutions (HEIs) is replete with these types of complaints. The work undertaken in this paper provides a solution to this problem. This paper proposes a simplified and efficient strategic planning model which executives can use to facilitate strategic planning in HEIs. This model takes into consideration, all the elements of previous models and synthesize them into a manageable, simplified framework that can be adapted to meet the planning needs of senior executives in any HEI.

Design/methodology/approach

The paper uses the action research framework to ground the solution to the problem identified. The action research framework is a sound research method that assists in resolving some of the practical problems executives in HEIs encounter as they move towards strategic planning. The researcher and a client in the higher educational sector, the UWI, engaged in collaborative problem-solving to develop a strategic plan for the client. To derive the solution, the researcher drew on the experience of the strategic planning process at the University of the West Indies (UWI) and also a number of selected universities in North American, Europe, Asia and Africa. The researcher then synthesized the outcomes from the deliberations and consultations with the client, the UWI and drew on theoretical knowledge in strategic management to derive the simplified model for strategic planning in higher education.

Findings

The research presented in this paper found that the existing strategic planning models used in higher education are generally complex, mostly designed specifically for an individual institution and lacks clarity regarding the implementation process. To overcome these problems for strategic planners in higher education, this paper proposes a simplified model that can be adapted by any HEI to assist with their strategic planning process. The Brainstoming- Visioning Action Results (B-VAR), the solution to the problem, presents the various elements of the strategic planning process that will need to be in place in order to develop a workable strategic plan and one that is implementable and will deliver tangible results for the HEI.

Originality/value

Besides adding to our knowledge in strategic management and specifically, strategic management in higher education, the greatest value from this paper is the solution it presents to solve the long-standing problem of having complex and ineffective planning models to lead strategic plan development in HEIs. The added value is that the model is integrative as it draws on elements of previous planning models but simplified them for their adaptation to any HEI.
Disaggregating emotional intelligence: building job satisfaction through emotional abilities
Authors: Winton Bradley Gene
Published: August 2021

Purpose

The changing environment of today’s organizations creates an atmosphere ripe for emotions. This ebb and flow of emotions need to be managed to facilitate positive outcomes such as job satisfaction. This paper aims to provide evidence that emotional intelligence directly impacts one’s satisfaction at work. This paper attempts to go beyond these higher-order findings to examine the dimensional aspects of emotional intelligence and the impact each one has on job satisfaction.

Design/methodology/approach

Using a quantitative survey conducted among 427 US-based workers, this paper tests a disaggregated emotional intelligence model and its hypothesized relationships with job satisfaction through structural equation modeling (SEM). Additional analysis includes confirmatory factor analysis (CFA) and a two-stage common method variance assessment.

Findings

The results confirmed the positive impact of the dimensions of emotional intelligence on job satisfaction. However, with interactive effects in place, the results also found signs of reciprocal suppression and could not confirm that all four emotional intelligence dimensions significantly and positively related to job satisfaction.

Originality/value

These findings are significant in that they are among the first to elaborate on the dimensions of emotional intelligence and their role in the improvement of one’s satisfaction at work. Further, these findings legitimize the use of the theoretical higher-order model of emotional intelligence in lieu of investigating its dimensional aspects.
Firms performance, risk taking and managerial ability
Authors: Simamora Alex Johanes
Published: August 2021

Purpose

This research aims to examine the moderating role of managerial ability on the relationship between risk-taking behavior and firms' performance.

Design/methodology/approach

This research uses 383 manufacturing firm-years listed on the Indonesian Stock Exchange as the research sample. The hypothesis test uses fixed-effect regression analysis.

Findings

The result shows that risk-taking behavior has a positive effect on firms' performance for higher managerial ability. Managerial ability provides higher knowledge, skill and information to get benefits and mitigate costs of risk-taking behavior to improve firms' performance. The role of managerial ability to make risk-taking behavior increase firms' performance occurs more for high-ability managers, dual CEO, shareholder-CEO and family CEO.

Originality/value

This research contributes to answering the conflicting arguments and filling the previous findings gap between risk-taking behavior and firm performance by considering managerial ability as a factor to create effective risk mitigation.