bluuebunny/crossref_metadata_2025_split huggingface dataset:
Route of oxytetracycline administration differentially impacts the growth and gut microbiome of pigs co-infected with Bordetella bronchiseptica and Pasteurella multocida
Authors: Mou Kathy T. , Trachsel Julian , Stephens Amali , Ricker Nicole , Brockmeier Susan L. , Allen Heather K. , Loving Crystal L. 
Published: April 2022

AbstractAlong with judicious antibiotic use, there is great interest in how the dose regimen of an antibiotic affects the animal gut microbiota. This study evaluated the impact of experimental respiratory infection alone or respiratory infection followed by oxytetracycline (oxytet) treatment on the animal’s health and its fecal microbiome. Piglets of approximately three weeks-of-age were separated into four groups (n=20 per group). One group remained non-infected and administered non-medicated feed and the other three groups were infected with Bordetella bronchiseptica (day 0) and Pasteurella multocida (day 4), with one group receiving non- medicated feed and the remaining two groups receiving oxytetr starting on day 7 by injection or in-feed (day 7-14). Infection with B. bronchiseptica and P. multocida negatively impacted piglet growth and induced mild pneumonia. Infection alone had minimal effect on the fecal microbiota community. When oxytet was administered either by injection or in-feed to treat the respiratory infections, both routes had minimal effect on clearing B. bronchiseptica and P. multocida in the animal. However, both routes appeared to limit lung lesion severity, and injected oxytet reduced the negative impact of infection on weight gain. Both routes had limited impact on the animal’s overall gut microbiome, including relative abundances of bacterial taxa and antibiotic resistance genes tet32, tetW, and aph2. Overall, oxytet administered by either route did not clear the respiratory infection, but oxytet administration minimized the negative health impacts of infection and had minor impact on the pig gut microbiome.ImportanceEfforts to address antibiotic resistance calls for improved antibiotic stewardship, including considering antibiotic administration route. While our previous study found in-feed oxytet had greater impact on the gut microbiome of healthy piglets than injected oxytet, it remained unknown if oxytet treatments would have the same impact on the microbiota of infected piglets. We evaluated the impact of respiratory infection alone or respiratory infection followed by oxytet treatment on the animals’ health and their gut microbiome profile. Respiratory infection negatively affected piglets’ health, but infection alone had minimal impact on the gut community. When oxytet was administered either in-feed or by injection to treat the respiratory infection, neither route of administration led to the clearance of the respiratory pathogens. However, oxytet minimized the negative health impacts of infection, and had minor impact on the pig gut microbiome. These findings are informative for disease management in food animals while integrating antibiotic stewardship practices.
Inducing Specific Chromosome Mis-Segregation in Human Cells
Authors: Tovini Laura , Johnson Sarah C. , Andersen Alexander M. , Spierings Diana Carolina Johanna , Wardenaar René , Foijer Floris , McClelland Sarah E. 
Published: April 2022

AbstractCancer cells display persistent underlying chromosomal instability that results in chromosome mis-segregation, the formation of micronuclei, and abnormal numbers of chromosomes (aneuploidy). These features are common to nearly all human cancers, with individual tumour types intriguingly exhibiting characteristic subsets of whole, and sub-chromosomal aneuploidies. To date, few methods to induce specific aneuploidies at will exist, hampering the investigation of functional consequences of recurrent aneuploidies. Moreover, although some human cell lines with specific aneuploidies exist, the acute cellular responses to specific chromosomal instability events remain unknown. We therefore investigated the possibility of sabotaging the mitotic segregation of specific chromosomes using nuclease-dead CRISPR-Cas9 (dCas9) as a cargo carrier to specific genomic loci. We recruited the kinetochore-nucleating domain of centromere protein CENP-T to assemble ectopic kinetochores either near the centromere of chromosome 9, or the telomere of chromosome 1. Ectopic kinetochore assembly led to increased chromosome instability and aneuploidy of the target chromosomes, providing the potential to create ‘designer karyotypes’ and study their immediate downstream cellular responses in a wide range of cell types. Overall, our findings provide new insights into ectopic kinetochore biology, and also represent an important step towards investigating the role of specific aneuploidy and chromosome mis-segregation events in diseases associated with aneuploidy.
Nucleosome sliding by the Chd1 chromatin remodeler relies on the integrity of the DNA duplex
Authors: Park Sangwoo , Ha Taekjip , Bowman Gregory D. 
Published: April 2022

ABSTRACTChromatin remodelers use a helicase-type ATPase motor to shift DNA around the histone core. Although not directly reading out the DNA sequence, some chromatin remodelers are biased by DNA sequences, suggesting that they may be sensitive to properties of the DNA duplex. Here, we present a high-throughput method for determining nucleosome positioning in vitro using site-specific DNA cleavage coupled with next-generation sequencing. This method allowed us to systematically test how the introduction of poly(dA:dT) tracts and other perturbations affected the distribution of nucleosomes remodeled by the Chd1 remodeler. We found that Chd1 is sensitive to poly(dA:dT) tracts as short as 3 bp, and that its nucleosome sliding activity is severely perturbed by DNA mismatches and single-nucleotide insertions. These results suggest that remodelers rely on the integrity of duplex DNA for nucleosome sliding. We also discovered that DNA on the nucleosome can shift in the absence of a remodeler when multiple mismatches are placed at superhelix location 2 (SHL2). This DNA movement in response to a disruption of the double helix may explain why SHL2 is the preferred site of engagement by most chromatin remodelers.
Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons
Authors: Lyons David B. , Briffa Amy , He Shengbo , Choi Jaemyung , Hollwey Elizabeth , Colicchio Jack , Anderson Ian , Feng Xiaoqi , Howard Martin , Zilberman Daniel 
Published: April 2022

AbstractCytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited over many generations. Such inheritance is thought to be mediated by a semiconservative mechanism that produces binary present/absent methylation patterns. However, we show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is stably inherited across many generations and is quantitatively associated with transposon expression. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably inherited at any level via a dynamic balance of these activities. We find that DRM2 – the core methyltransferase of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive de novo methylation.
C. elegans Sine oculis/SIX-type homeobox genes act as homeotic switches to define neuronal subtype identities
Authors: Cros Cyril , Hobert Oliver 
Published: April 2022

ABSTRACTThe classification of neurons into distinct types reveals hierarchical taxonomic relationships that reflect the extent of similarity between neuronal cell types. At the base of such taxonomies are neuronal cells that are very similar to one another but differ in a small number of reproducible and select features. How are very similar members of a neuron class that share many features instructed to diversify into distinct subclasses? We show here that the six very similar members of the C. elegans IL2 sensory neuron class, which are all specified by a homeobox terminal selector, unc-86/BRN3A/B, differentiate into two subtly distinct subclasses, a dorsoventral subclass and a lateral subclass, by the toggle switch-like action of the SIX/Sine-oculis homeobox gene unc-39. unc-39 is expressed only in the lateral IL2 neurons and loss of unc-39 leads to a homeotic transformation of the lateral into the dorsoventral class; conversely, ectopic unc-39 expression converts the dorsoventral subclass into the lateral subclass. Hence, a terminal selector homeobox gene controls both class-, as well as subclass-specific features, while a subordinate homeobox gene determines the ability of the class-specific homeobox gene to activate subtype-specific target genes. We find a similar regulatory mechanism to operate in a distinct class of six motor neurons. Our findings underscore the importance of homeobox genes in neuronal identity control and invite speculations about homeotic identity transformations as potential drivers of evolutionary novelty during cell type evolution in the brain.SIGNIFICANCE STATEMENTAnatomical and molecular studies have revealed that in many animal nervous systems, neuronal cell types can often be subclassified into highly related subtypes with only small phenotypic differences. We decipher here the regulatory logic of such cell type diversification processes. We show that identity features of neurons that are highly similar to one another are controlled by master regulatory transcription factors and that phenotypic differences between related cell types are controlled by downstream acting transcription factors that promote or antagonize the ability of such a master regulatory factor to control unique identity features. Our findings help explain how neuronal cell types diversify and suggest hypothetical scenarios for neuronal cell type evolution.
The Spike protein of SARS-CoV-2 impairs lipid metabolism and increases susceptibility to lipotoxicity: implication for a role of Nrf2
Authors: Nguyen Vi , Zhang Yuping , Gao Chao , Cao Xiaoling , Tian Yan , Carver Wayne , Kiaris Hippokratis , Cui Taixing , Tan Wenbin 
Published: April 2022

AbstractBackground/objectivesCoronavirus disease 2019 (COVID-19) patients exhibit lipid metabolic alterations, but the mechanism remains unknown. In this study, we aimed to investigate whether the Spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) impairs lipid metabolism in host cells.MethodsA Spike cell line in HEK293 was generated using the pcDNA vector carrying the Spike gene expression cassette. A control cell line was generated using the empty pcDNA vector. Gene expression profiles related to lipid metabolic, autophagic, and ferroptotic pathways were investigated. Palmitic acid (PA)-overload was used to assess lipotoxicity-induced necrosis.ResultsAs compared with controls, the Spike cells showed a significant increase in lipid depositions on cell membranes as well as dysregulation of expression of a panel of molecules involved lipid metabolism, autophagy, and ferroptosis. The Spike cells showed an upregulation of nuclear factor erythroid 2-related factor 2 (Nrf2), a multifunctional transcriptional factor, in response to PA. Furthermore, the Spike cells exhibited increased necrosis in response to PA-induced lipotoxicity compared to control cells in a time- and dose-dependent manner via ferroptosis, which could be attenuated by the Nrf2 inhibitor trigonelline.ConclusionsThe Spike protein impairs lipid metabolic and autophagic pathways in host cells, leading to increased susceptibility to lipotoxicity via ferroptosis which can be suppressed by a Nrf2 inhibitor. This data also suggests a central role of Nrf2 in Spike-induced lipid metabolic impairments.HighlightsThe Spike protein increases lipid deposition in host cell membranesThe Spike protein impairs lipid metabolic and autophagic pathwaysThe Spike protein exaggerates PA-induced lipotoxicity in host cells via ferroptosisNrf2 inhibitor Trigonelline can mitigate the Spike protein-induced necrosis
Weak tension accelerates hybridization and dehybridization of short oligonucleotides
Authors: Hart Derek J. , Jeong Jiyoun , Gumbart James C. , Kim Harold D. 
Published: April 2022

AbstractThe hybridization and dehybridization of DNA subject to tension is relevant to fundamental genetic processes and to the design of DNA-based mechanobiology assays. While strong tension accelerates DNA melting and decelerates DNA annealing, the effects of tension weaker than 5 pN are less clear. In this study, we developed a DNA bow assay, which uses the bending rigidity of double-stranded DNA (dsDNA) to exert weak tension on a single-stranded DNA (ssDNA) target in the range of 2pN to 6pN. Combining this assay with single-molecule FRET, we measured the hybridization and dehybridization kinetics between a 15 nt ssDNA under tension and a 8-9 nt oligo, and found that both the hybridization and dehybridization rates monotonically increase with tension for various nucleotide sequences tested. These findings suggest that the nucleated duplex in its transition state is more extended than the pure dsDNA or ssDNA counterpart. Our simulations using the coarse-grained oxDNA2 model indicate that the increased extension of the transition state is due to exclusion interactions between unpaired ssDNA regions in close proximity to one another. This study highlights an example where the ideal worm-like chain models fail to explain the kinetic behavior of DNA in the low force regime.
Binding of the peptide deformylase on the ribosome surface modulates the structure and dynamics of the exit tunnel interior
Authors: McGrath Hugo , Černeková Michaela , Kolář Michal H. 
Published: April 2022

AbstractProteosynthesis on ribosomes is regulated at many levels. Conformational changes of the ribosome, possibly induced by external factors, may transfer over large distances and contribute to the regulation. The molecular principles of this long-distance allostery within the ribosome remain poorly understood. Here, we use structural analysis and atomistic molecular dynamics simulations to investigate peptide deformylase (PDF), an enzyme that binds to the ribosome surface near the ribosomal protein uL22 during translation and chemically modifies the emerging nascent peptide. Our simulations of the entire ribosome–PDF complex reveal that the PDF undergoes a swaying motion on the ribosome surface at the sub-microsecond time scale. We show that the PDF affects the conformational dynamics of parts of the ribosome over distances of more than 5 nm. Using a supervised-learning algorithm we demonstrate that the exit tunnel is influenced by the presence or absence of PDF. Our findings suggest a possible effect of the PDF on the nascent peptide translocation through the ribosome exit tunnel.
Fast-converging chain-cluster-based routing protocols using the Red-Deer Algorithm in Wireless Sensor Networks
Authors: Dayal Kamalakshi , Bassoo Vandana 
Published: April 2022

PurposeThe performance of Wireless Sensor Networks (WSNs) applications is bounded by the limited resources of battery-enabled Sensor Nodes (SNs), which include energy and computational power; the combination of which existing research seldom focuses on. Although bio-inspired algorithms provide a way to control energy usage by finding optimal routing paths, those which converge slower require even more computational power, which altogether degrades the overall lifetime of SNs.Design/methodology/approachHence, two novel routing protocols are proposed using the Red-Deer Algorithm (RDA) in a WSN scenario, namely Horizontal PEG-RDA Equal Clustering and Horizontal PEG-RDA Unequal Clustering, to address the limited computational power of SNs. Clustering, data aggregation and multi-hop transmission are also integrated to improve energy usage. Unequal clustering is applied in the second protocol to mitigate the hotspot problem in Horizontal PEG-RDA Equal Clustering.FindingsComparisons with the well-founded Ant Colony Optimisation (ACO) algorithm reveal that RDA converges faster by 85 and 80% on average when the network size and node density are varied, respectively. Furthermore, 33% fewer packets are lost using the unequal clustering approach which also makes the network resilient to node failures. Improvements in terms of residual energy and overall network lifetime are also observed.Originality/valueProposal of a bio-inspired algorithm, namely the RDA to find optimal routing paths in WSN and to enhance convergence rate and execution time against the well-established ACO algorithm. Creation of a novel chain cluster-based routing protocol using RDA, named Horizontal PEG-RDA Equal Clustering. Design of an unequal clustering equivalent of the proposed Horizontal PEG-RDA Equal Clustering protocol to tackle the hotspot problem, which enhances residual energy and overall network lifetime, as well as minimises packet loss.
Willingness to eat ethnic foods and food experience: a study on Khasi Food
Authors: Mawroh Hakamelamphylla , Dixit Saurabh Kumar 
Published: April 2022

PurposeThe present study analyses Khasi Food as an ethnic food to be promoted as a tourism product encouraging tourists to visit Meghalaya, India. The food tourists are primarily motivated to eat Khasi Food to provide authentic ethnic food experiences. Therefore, the purpose of the paper is to explore the willingness of tourists to eat ethnic foods and the consequent ethnic Khasi Food Experience (KFE).Design/methodology/approachThis paper adopts a convergent triangulation approach. Statistical data analysis and thematic analysis were incorporated, and the combined results were compared to see if they converged to achieve the same objective or purpose, which is willingness to eat ethnic foods that influences KFE in the study area (selected villages in East Khasi Hills District and West Jaiñtia Hills District).FindingsThe converged findings from statistical analysis and thematic analysis indicate that tourists who visited the study area were willing to eat ethnic foods, which is Khasi Food and their willingness to do so has a positive influence on KFE.Originality/valueTo the best of the authors’ knowledge, this paper is original and the first of its kind because this study has not been conducted yet in the state of Meghalaya, India. This paper has an authentic value of projecting Khasi Food globally as a cultural and ethnic tourism product giving meaningful experiences to tourists and locals alike.
Incomes, employment and gender roles: understanding women's intrahousehold decision-making participation in Nicaragua
Authors: Gómez-Valle Roxana , Holvoet Nathalie 
Published: April 2022

PurposeThis paper explores the relationship between married women's intrahousehold decision-making participation and marital gender roles, next to factors suggested in the household bargaining literature. Additionally, the authors investigate whether women's employment carries the same importance for decision-making participation as contributions to household incomes.Design/methodology/approachUsing 2011/2012 Nicaraguan Demographic and Health Survey (DHS), the authors estimate multinomial logistic regressions for eight decision-making domains, analyzing three levels of decision-making: wife-dominant or sole decisions, joint decision-making (with the partner) and decision-making by someone else. The authors create an additive index for measuring internalized marital gender roles.FindingsWomen's intrahousehold decision-making participation is explained differently depending on the decision-making area and level of participation. Women with a better relative position vis-à-vis partners and not following patriarchal gender roles are more likely to make decisions jointly with their partners, but not alone. Women's age and educational level are the strongest predictors in the analysis. Women's employment reduces their decision-making participation in children's disciplining and daily cooking-related decisions.Research limitations/implicationsIt focuses on married women only, while marital status might be a determinant of decision-making itself and left out the contribution of unearned incomes.Practical implicationsInterventions aimed at increasing women's intrahousehold decision-making participation should not only focus on economic endowments but also comprehend the gendered dynamics governing intrahousehold allocation.Originality/valueThe study incorporates quantitative measures of marital gender roles in the study of intrahousehold decision-making. It also contributes to the literature with insights from contexts where women's involvement in employment increased against a background of patriarchal gender roles.
Image needs of Pakistani visual artists in an academic setting abstract
Authors: Hussain Syed Tauseef , Soroya Saira Hanif , Ameen Kanwal 
Published: April 2022

Purpose
This study aims to explore visual artists’ image needs and the obstacles they face in meeting them.

Design/methodology/approach
The visual artists, participating in the study, included painters, graphic designers, textile designers, architects and sculptors who were faculty members in two oldest art institutions of Pakistan. A total of 20 face-to-face interviews representing four participants from each visual artists group were conducted. The textual data were analyzed thematically, using NVIVO 12 software.

Findings
Results showed that under-study visual artists need images mainly for academic purposes (teaching, assignments, etc.) and for professional and research purposes. However, they require images quite often, as a majority of the respondents told that they need images on daily basis.

Social implications
The study findings provide an insight for information science professionals, system designers and image librarians regarding visual artists’ image using behavior.

Originality/value
As the researchers could not find any such study in local context, and a very few globally, therefore, this study may serve as a baseline for further research in this area.
The effects of IMF programs on income inequality: a semi-parametric treatment effects approach
Authors: Chletsos Michael , Sintos Andreas 
Published: April 2022

PurposeThis paper aims to provide new insights regarding the impact of International Monetary Fund (IMF) programs on income inequality.Design/methodology/approachThe paper uses a novel methodological approach proposed by Acemogluet al.(2019), using (1) the regression adjustment, (2) the inverse probability weighting and (3) the doubly robust estimator, which combines (1) and (2), and a sample of annual data for 135 developing countries over the time period 1970 to 2015.FindingsThe findings show that IMF programs are associated with greater income inequality for up to five years. By differentiating the effect of IMF programs, the authors find that only IMF non-concessional programs have a significant detrimental effect on income inequality, while IMF concessional programs do not have a consistent effect on income inequality. In addition, the authors find that only IMF programs with a higher number of conditions have a detrimental and statistically significant effect on income inequality, compared to IMF programs with a smaller number of conditions, where their effect on income inequality is found to be insignificant.Originality/valueTo the best of the authors’ knowledge, the analysis developed in this paper contributes to the existing literature by applying the most methodologically sound identification strategy, which does not rely on the linearity assumption, the selection of instruments or matching variables and additionally takes into account the selection bias related to IMF program participation.