bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tissue-specific Genome Editing in vivo by MicroRNA-repressible Anti-CRISPR Proteins
Authors: Lee Jooyoung , Mou Haiwei , Ibraheim Raed , Liang Shun-Qing , Xue Wen , Sontheimer Erik 
Published: May 2019

AbstractCRISPR-Cas systems are bacterial adaptive immune pathways that have revolutionized biotechnology and biomedical applications. Despite the potential for human therapeutic development, there are many hurdles that must be overcome before its use in clinical settings. Some clinical safety concerns arise from persistent activity of Cas9 after the desired editing is complete, or from editing activity in unintended cell types or tissues upon in vivo delivery [e.g. by adeno-associated viruses (AAV)]. Although tissue-specific promoters and serotypes with tissue tropisms can be used, suitably compact promoters are not always available for desired cell types, and AAV tissue tropisms are not absolute. To reinforce tissue-specific editing, we exploited anti-CRISPR proteins (Acrs), which are proteins evolved as countermeasures against CRISPR immunity. To inhibit Cas9 in all ancillary tissues without compromising editing in the target tissue, we established a flexible platform in which an Acr transgene is repressed by endogenous, tissue-specific microRNAs (miRNAs). We demonstrate that miRNAs regulate the expression of an Acr transgene bearing miRNA-binding sites in its 3’ UTR, and control subsequent genome editing outcomes in a cell-type specific manner. We also show that the strategy is applicable to multiple Cas9 orthologs and their respective Acrs. Furthermore, we demonstrate that in vivo delivery of Cas9 and Acrs that are targeted for repression by liver-specific miR-122 allow editing in the liver while Acrs devoid of miRNA regulation prevent Cas9 activity. This strategy provides additional safeguards against off-tissue genome editing by confining Cas9 activity to selected cell types.
Dietary restriction improves fitness of ageing parents but reduces fitness of their offspring
Authors: Mautz Brian S. , Lind Martin I. , Maklakov Alexei A. 
Published: May 2019

AbstractDietary restriction (DR) is a well-established intervention to extend lifespan across taxa. Recent studies suggest that DR-driven lifespan extension can be cost-free, calling into question a central tenant of the evolutionary theory of ageing. Nevertheless, boosting parental longevity can reduce offspring fitness. Such intergenerational trade-offs are often ignored but can account for the ‘missing costs’ of longevity. Here, we use the nematode Caenorhabditis remanei to test for effects of DR by fasting on fitness of females and their offspring. Females deprived of food for six days indeed had increased fecundity, survival and stress resistance after re-exposure to food compared to their counterparts with constant food access. However, offspring of DR mothers had reduced early and lifetime fecundity, slower growth rate, and smaller body size at sexual maturity. These findings support the direct trade-off between investment in soma and gametes challenging the hypothesis that increased somatic maintenance and impaired reproduction can be decoupled.
Patterned substrates modulate growth and dynamics of 3D cellular systems
Authors: Fanous Michael J. , Li Yanfen , Kandel Mikhail E. , Kilian Kristopher A. , Popescu Gabriel 
Published: May 2019

AbstractThe development of 3D cellular architectures during development and pathological processes involves intricate migratory patterns that are modulated by genetics and the surrounding microenvironment. The substrate composition of cell cultures has been demonstrated to influence growth, proliferation, and migration in 2D. Here we study the growth and dynamics of mouse embryonic fibroblast (MEF) cultures patterned in a tissue sheet which then exhibits 3D growth. Using gradient light interference microscopy (GLIM), a label-free quantitative phase imaging approach, we explored the influence of geometry on cell growth patterns and rotational dynamics. We apply, for the first time to our knowledge, dispersion-relation phase spectroscopy (DPS) in polar coordinates to generate the radial and rotational cell mass-transport. Our data show that cells cultured on engineered substrates undergo rotational transport in a radially independent manner and exhibit faster vertical growth than the control, unpatterned cells. The use of GLIM and polar DPS provides a novel quantitative approach to studying the effects of spatially patterned substrates on cell motility and growth.
Assembly Mechanisms of Neotropical Butterfly Communities Along an Environmental Gradient
Authors: Checa María F. , Donoso David , Levy Elisa , Mena Sebastián , Rodriguez Jaqueline , Willmott Keith 
Published: May 2019

AbstractOur goal was to test the hypothesis that assembly processes that limit species similarity (i.e., competition) predominantly occur in more ‘stable’ abiotic environments, whereas habitat filtering (i.e., habitat characteristics) is a major driver of community composition within more variable environments at regional (e.g., aseasonal vs seasonal forests) and local scales (e.g., understory vs. canopy). A combined approach of phylogenetic- and functional trait-based analyses using forewing length and aspect ratio as traits, were used to this hypothesis.A 3-year survey was carried out at three sites (i.e., wet, transition and dry forests) across a climatic gradient in western Ecuador. Transition and dry forests were considered as seasonal, whereas wet forest were considered aseasonal. Butterflies were sampled using traps baited with rotting banana and prawn every two months from Nov 2010 to Sep 2013. Traps were set up at two heights, in the understory and canopy. DNA was extracted to sequence the barcode’ section of the mitochondrial gene cytochrome oxidase 1 (COI) for phylogenetic analyses. Measurements of morphological traits, forewing length and aspect ratio were done using digital photographs of specimens.A total of 6466 specimens representing 142 species of Nymphalidae were recorded. Based on phylogenetic- and trait-based analyses, we rejected the hypothesis that assembly processes that limit species similarity (i.e., competition) are likely to predominantly occur in more ‘stable’ abiotic environments, whereas habitat filtering can be a major driver of community composition within more variable environments at regional (i.e., aseasonal forest vs seasonal forests) and local scales (i.e., understory vs. canopy). My study of assembly mechanisms revealed the opposite pattern, with stronger evidence for the action of ecological filters in the assembly of butterfly communities from the wet aseasonal forests, and competition likely to be a major assembly process within dry seasonal forests. The present study therefore provided new insights into community assembly mechanisms in one of the richest butterfly faunas worldwide.
Medial entorhinal cortex activates in a traveling wave
Authors: Hernández-Pérez J.J. , Cooper K.W. , Newman E.L. 
Published: May 2019

SummaryTraveling waves of cortical activity are hypothesized to organize cortical information processing and support interregional communication. Yet, it remains unknown whether interacting areas exhibit the matched traveling waves necessary to support this hypothesized form of interaction. Here, we show that the strongly-interacting medial entorhinal cortex (MEC) and hippocampus exhibit matched traveling waves. We demonstrate that both the field potential and spiking in the MEC exhibit prominent 6-12 Hz ‘theta’ traveling waves matching those of the hippocampus. The theta phase shifts observed along the MEC were accounted for largely by variation in waveform asymmetry. From this, we hypothesize that that gradients in local physiology underlie both the generation of MEC traveling waves and the functional variations observed previously across the MEC.
Comparing low-pass sequencing and genotyping for trait mapping in pharmacogenetics
Authors: Wasik Kaja , Berisa Tomaz , Pickrell Joseph K. , Li Jeremiah H. , Fraser Dana J. , King Karen , Cox Charles 
Published: May 2019

AbstractLow pass sequencing has been proposed as a cost-effective alternative to genotyping arrays to identify genetic variants that influence multifactorial traits in humans. For common diseases this typically has required both large sample sizes and comprehensive variant discovery. Genotyping arrays are also routinely used to perform pharmacogenetic (PGx) experiments where sample sizes are likely to be significantly smaller, but clinically relevant effect sizes likely to be larger. To assess how low pass sequencing would compare to array based genotyping for PGx we compared a low-pass assay (in which 1× coverage or less of a target genome is sequenced) along with software for genotype imputation to standard approaches. We sequenced 79 individuals to 1× genome coverage and genotyped the same samples on the Affymetrix Axiom Biobank Precision Medicine Research Array (PMRA). We then down-sampled the sequencing data to 0.8×, 0.6×, and 0.4× coverage, and performed imputation. Both the genotype data and the sequencing data were further used to impute human leukocyte antigen (HLA) genotypes for all samples. We compared the sequencing data and the genotyping array data in terms of four metrics: overall concordance, concordance at single nucleotide polymorphisms in pharmacogenetics-related genes, concordance in imputed HLA genotypes, and imputation r2. Overall concordance between the two assays ranged from 98.2% (for 0.4× coverage sequencing) to 99.2% (for 1× coverage sequencing), with qualitatively similar numbers for the subsets of variants most important in pharmacogenetics. At common single nucleotide polymorphisms (SNPs), the mean imputation r2from the genotyping array was 90%, which was comparable to the imputation r2from 0.4× coverage sequencing, while the mean imputation r2from 1× sequencing data was 96%. These results indicate that low-pass sequencing to a depth above 0.4× coverage attains higher power for trait mapping when compared to the PMRA.
Kinetic characteristics of propofol-induced inhibition of electron-transfer chain and fatty acid oxidation in human and rodent skeletal and cardiac muscles
Authors: Urban Tomáš , Waldauf Petr , Krajčová Adéla , Jiroutková Kateřina , Halačová Milada , Džupa Valér , Janoušek Libor , Pokorná Eva , Duška František 
Published: May 2019

AbstractIntroductionPropofol causes a profound inhibition of fatty acid oxidation (FAO) and reduces spare electron transfer chain (ETC) capacity in a range of human and rodent cells and tissues – a feature that might be related to the pathogenesis of Propofol Infusion Syndrome. We aimed to explore the mechanism of propofol-induced alteration of bioenergetic pathways by describing its kinetic characteristics.MethodsWe obtained samples of skeletal and cardiac muscle from Wistar rat (n=3) and human subjects: vastus lateralis from hip surgery patients (n=11) and myocardium from brain-dead organ donors (n=10). We assessed mitochondrial functional indices using standard SUIT protocol and high resolution respirometry in fresh tissue homogenates with or without short-term exposure to a range of propofol concentration (2.5-100 μg/ml). After finding concentrations of propofol causing partial inhibition of a particular pathways, we used that concentration to construct kinetic curves by plotting oxygen flux against substrate concentration during its stepwise titration in the presence or absence of propofol. By spectrophotometry we also measured the influence of the same propofol concentrations on the activity of isolated respiratory complexes.ResultsWe found that human muscle and cardiac tissues are more sensitive to propofol-mediated inhibition of bioenergetic pathways than rats tissue. In human homogenates, palmitoyl carnitine-driven respiration was inhibited at much lower concentrations of propofol than that required for a reduction of ETC capacity, suggesting FAO inhibition mechanism different from downstream limitation or carnitine-palmitoyl transferase-1 inhibition. Inhibition of Complex I was characterised by more marked reduction of Vmax, in keeping with non-competitive nature of the inhibition and the pattern was similar to the inhibition of Complex II or ETC capacity. There was no inhibition of Complex IV nor increased leak through inner mitochondrial membrane with up to 100 μg/ml of propofol. If measured in isolation by spectrophotometry, propofol 10 μg/ml did not affect the activity of any respiratory complexes.ConclusionIn human skeletal and heart muscle homogenates, propofol in concentrations that are achieved in propofol-anaesthetized patients, causes a direct inhibition of fatty acid oxidation, in addition to inhibiting flux of electrons through inner mitochondrial membrane. The inhibition is more marked in human as compared to rodent tissues.
A competence-regulated toxin-antitoxin system inHaemophilus influenzae
Authors: Black Hailey Findlay , Mastromatteo Scott , Sinha Sunita , Ehrlich Rachel L. , Nislow Corey , Mell Joshua Chang , Redfield Rosemary J. 
Published: May 2019

ABSTRACTNatural competence allows bacteria to respond to environmental and nutritional cues by taking up free DNA from their surroundings, thus gaining both nutrients and genetic information. In the Gram-negative bacteriumHaemophilus influenzae, the genes needed for DNA uptake are induced by the CRP andSxytranscription factors in response to lack of preferred carbon sources and nucleotide precursors. Here we show that one of these genes,HI0659, encodes the antitoxin of a competence-regulated toxin-antitoxin operon (‘toxTA’), likely acquired by horizontal gene transfer from aStreptococcusspecies. Deletion of the putative toxin(HI0660)restores uptake to the antitoxin mutant. The fulltoxTAoperon was present in only 17 of the 181 strains we examined; complete deletion was seen in 22 strains and deletions removing parts of the toxin gene in 142 others. In addition to the expected Sxy-and CRP-dependent-competence promoter,HI0659/660transcript analysis using RNA-seq identified an internal antitoxin-repressed promoter whose transcription starts withintoxTand will yield nonfunctional protein. We propose that the most likely effect of unopposed toxin expression is non-specific cleavage of mRNAs and arrest or death of competent cells in the culture. Although the high frequency oftoxTandtoxTAdeletions suggests that this competence-regulated toxin-antitoxin system may be mildly deleterious, it could also facilitate downregulation of protein synthesis and recycling of nucleotides under starvation conditions. Although our analyses were focused on the effects oftoxTA, the RNA-seq dataset will be a useful resource for further investigations into competence regulation.ABBREVIATED SUMMARYThe competence regulon ofHaemophilus influenzaeincludes an unprecedented toxin/antitoxin gene pair. When not opposed by antitoxin, the toxin completely prevents DNA uptake but causes only very minor decreases in cell growth and competence gene expression. The TA gene pair was acquired by horizontal gene transfer, and the toxin gene has undergone repeated deletions in other strains.
Perceived managerial and leadership effectiveness in Mexico and the USA
Authors: Ruiz Carlos Enrique , Hamlin Bob 
Published: May 2019

PurposeThe purpose of this study was to compare the perceptions of Mexican and US employees about effective and ineffective managerial behaviour.Design/methodology/approachA qualitative multiple cross-case comparative analysis of findings obtained from two past emic replication studies of observed effective and ineffective managerial behaviour carried out in Mexico and the USA respectively was conducted.FindingsNotwithstanding the significant cultural variances between Mexico and the USA underlined by various cross-cultural studies, the findings suggest that Mexican and US employees perceive effective and ineffective managerial behaviour in a very similar manner.Research limitations/implicationsWhile the results of the study suggest that culture may not play a significant role in the way people perceive managerial and leadership effectiveness, the authors suggest that more replication studies with larger and more balanced gender samples using different methods need to be performed in both countries.Practical implicationsThe findings of the study may be relevant for human resource development professionals in both countries when providing training to expatriates for international assignments. Reinforcing the set of managerial practices that are perceived as effective in these two countries and emphasizing those practices that may be particular to Mexico and the USA respectively, could lead to an improvement in the performance of Mexican executives managing in the USA and US executives managing in Mexico.Originality/valueThis paper compares managerial behavioural effectiveness between Mexico and the USA.
Patterns and trends in engineering education in sustainability
Authors: Tejedor Gemma , Rosas-Casals Martí , Segalas Jordi 
Published: May 2019

Purpose
This paper aims to identify patterns and trends taking place in engineering education in sustainability, through analyzing the evolution of research conducted in relevant publications in the field of engineering education for sustainability in the past decades.

Design/methodology/approach
First, a bibliometric approach has been applied, adopting a co-word analysis based on co-occurrence of the keywords (300 items) in articles from three indexed journals related to engineering, education or sustainability. The selection of the articles has been based on the appearance of the previous three terms in the topic and title fields of the journal, where journal scope (based in the categories of the InCites Journal Citation Reports) covered at least two topics, and the third topic was applied in the search, as follows: International Journal of Sustainability in Higher Education – Scope of the journal: sustainability and education, Keyword search: engineering (20 papers); Journal of Cleaner Production – Scope of the journal: sustainability and engineering, Keyword search: education (122 papers); International Journal of Engineering Education – Scope of the journal: engineering and education, Keyword search: sustainability (29 papers); Second, to identify topological patterns and their evolution, a structural and temporal analysis of the network of keywords and a categorization of the keywords in thematic clusters (named categories) have been performed.

Findings
The most relevant categories in terms of corresponding number of keywords, even though these have decreased in recent years, are those related with institutional and policy aspects to embedding or applying sustainability in higher education. At the same time, categories related to the professional development of faculty members, implementation and use of learning strategies (i.e. real-world learning experiences, educational innovative initiatives/tools/techniques) and cross-boundary schemes (i.e. transdisciplinarity, ethics, networking, etc.) increase their relevance in the past five years, signaling some of the challenging fields of interest in engineering higher education in sustainability in the near future.

Practical implications
Knowledge of the trends in devising sustainability education in engineering allows for designing curricular schemes and learning strategies to achieve competences, which are key factors for the change toward sustainability.

Originality/value
This research has a strong strategic value, as it indicates the focus of future research efforts and networking on some of the topics of greatest concern in engineering higher education for sustainability.
The effects of video game making within science content on student computational thinking skills and performance
Authors: Garneli Varvara , Chorianopoulos Konstantinos 
Published: May 2019

PurposeThis study aims to explore the effects of an alternative learning environment, such as the video game making (VGM) within science content, on computational thinking (CT) skills development and student performance.Design/methodology/approachA didactic intervention was performed for five weeks. Two student groups were taught the same computational concepts in two ways. One group was taught by constructing a video game within science content to practice science and computing curriculum while the other group constructed appropriately designed projects to practice only the computing curriculum. Additionally, the students constructed a pretest project before the beginning of the intervention and a post-test project after its end. Results were based on quantitative and qualitative code analysis and interviews from the students.FindingsVGM within science content resulted in projects with more CT skills and also supported students to effectively apply their acquired coding skills, after the end of the intervention.Practical implicationsThe results of this study suggest an interdisciplinary environment, such as the VGM within science content, which can effectively support CT skills development and computing curriculum.Originality/valueAlthough VGM has been successfully applied to teach science content, this study explored the potential influence of this learning environment on CT skills development and coding fluency. Such interdisciplinary educational environments could be applied in the typical school settings to promote a plethora of skills and academic contents.
Opportunities and challenges for NGOs amid competing institutional logics
Authors: Glazer Joshua L. , Groth Laura , Beuche Blair 
Published: May 2019

PurposeThis paper considers the implications of reform efforts that rely on charter management organizations to assume operational control of underperforming neighborhood schools. The purpose of this paper is to examine the way in which changes to the education sector place enormous pressure on these organizations to both manage instruction and their social environments.Design/methodology/approachThe research presents the results from a longitudinal case study of two organizations operating within the Tennessee Achievement School District (ASD). Interviews, observations and document analysis provided insight into the perspectives of school operators, state officials and community leaders. The study design allowed researchers to observe the influence of the environment on school operators over a four-year period.FindingsResults show that the environment that included a muscular state, market pressures, NGOs and local communities placed an extreme and contradictory set of demands on organizations operating schools, pressing them to develop robust systems of instruction, leadership and teacher development while actively working to ensure social legitimacy in the community. Neither a national network nor a small local startup began with a strategy aligned to these environmental demands, and both needed to make substantial revisions.Research limitations/implicationsResearch into contemporary educational reform should account for rapidly evolving environments that feature a complex mix of resources and incentives. Careful examination of the consequences of these environments for educational organizations will further our understanding of how markets, communities and governments are shaping the education sector.Practical implicationsThe extraordinary challenges that confront organizations that operate in crowded and contested environments preclude fast or dramatic results. Policymakers and the public should assume an incremental process of organizational learning and improvement. Setting unrealistic expectations and focusing exclusively on impact risks delegitimizing organizations and policy initiatives before they have time to adapt.Originality/valueThis research reported here is among the few studies that have explored the experiences and implications of NGOs that have attempted to assume operational control of underperforming neighborhood schools. The popularity of this approach among a growing number of states highlights the importance of this topic.