bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

SummaryBacteria 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 costHighlightsMutants with only 3 ribosomal operons grow faster than wild-type in minimal mediumΔ4 rrn and rpoB mutants share phenotypic traitsFaster growth of mutants is achieved by increased ribosome contentFast-growing mutants display reduced hedging expression and adaptation trade-offsDespite 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

AbstractA 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-Fungal isolates from brewery microbiota were screened for beer production-Numerous maltose-negative strains were tested for low-alcohol beer fermentation-Trigonopsis cantarelliishowed promise compared to a commercial reference strain-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

ABSTRACTMicrosatellites 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

AbstractThe 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.
MVsim: a toolset for quantifying and designing multivalent interactions
Authors: Bruncsics Bence , Errington Wesley J. , Sarkar Casim A. 
Published: August 2021

AbstractArising 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

AbstractThe 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

ABSTRACTHistone 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

AbstractPlants 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

AbstractA 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 summaryThe 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.
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

PurposeThis 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/approachThe 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.FindingsThe 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/valueThis 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

PurposeInequality 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/approachThe 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.FindingsLived 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/valueThe 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

PurposeThe 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/approachThe 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.FindingsThe 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/valueThe 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

PurposeEntrepreneurship 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/approachData 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.FindingsEconomics, 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/valueThis 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.