bluuebunny/crossref_metadata_2025_split huggingface dataset:
FtsK, a DNA motor protein, coordinates the genome segregation and early cell division processes in Deinococcus radiodurans
Authors: Mishra Shruti , Misra Hari S. , Kota Swathi 
Published: July 2022

AbstractFtsK/SpoIIIE protein family are DNA translocases known as the fastest DNA motor proteins that use ATP for their movement on DNA. Most of the studies in single chromosome-containing bacteria have established the role of FtsK in chromosome dimer resolution (CDR) connecting the bacterial chromosome segregation process with cell division. But, only limited reports are available on the interdependent regulation of genome segregation and cell division in multipartite genome harbouring (MGH) bacteria. In this study, for the first time, we report the characterization of FtsK from the radioresistant MGH bacterium Deinococcus radiodurans R1 (drFtsK). drFtsK shows the activity characteristics of a typical FtsK/SpoIIIE/Tra family. It stimulates the site-specific recombination catalyzed by Escherichia coli tyrosine recombinases. drFtsK interacts with various cell division and genome segregation proteins of D. radiodurans. Microscopic examination of different domain deletion mutants of this protein reveals alterations in cellular membrane architecture and nucleoid morphology. In-vivo localization studies of drFtsK-RFP show that it forms multiple foci on nucleoid as well as on the membrane with maximum density on the septum. drFtsK coordinates its movement with nucleoid separation. The alignment of its foci shifts from old to new septum indicating its cellular dynamics with the FtsZ ring during the cell division process. Nearly, similar positional dynamicity of FtsK was observed in cells recovering from gamma radiation exposure. These results suggest that FtsK forms a part of chromosome segregation, cell envelope, and cell division machinery in D. radiodurans.ImportanceDeinococcus radiodurans show extraordinary resistance to γ-radiation. It is polyploid and harbours a multipartite genome comprised of two chromosomes and two plasmids, packaged in a doughnut-shaped toroidal nucleoid. Very little is known about how the tightly packed genome is accurately segregated and the next divisional plane is determined. FtsK, a multifunctional protein, helps in pumping the septum-trapped DNA in several bacteria. Here, we characterized FtsK of D. radiodurans R1 (drFtsK) for the first time and showed it to be an active protein. The absence of drFtsK causes many defects in morphology at both cellular and nucleoid levels. The compact packaging of the deinococcal genome and cell membrane formation is hindered in ftsK mutants. In-vivo drFtsK is dynamic, forms foci on both nucleoid and septum, and coordinates with FtsZ for the next cell division. Thus, drFtsK role in maintaining the normal genome phenotype and cell division in Deinococcus radiodurans is suggested.
Allele-specific expression reveals multiple paths to highland adaptation in maize
Authors: Hu Haixiao , Crow Taylor , Nojoomi Saghi , Schulz Aimee J. , Hufford Matthew B. , Flint-Garcia Sherry , Sawers Ruairidh , Rellan-Alvarez Ruben , Estévez-Palmas Juan M. , Ross-Ibarra Jeffrey , Runcie Daniel E. 
Published: July 2022

AbstractMaize is a staple food of smallholder farmers living in highland regions up to 4,000 meters above sea level worldwide. Mexican and South American highlands are two major highland maize growing regions, and population genetic data suggests the maize’s adaptation to these regions occurred largely independently, providing a case study for parallel evolution. To better understand the mechanistic basis of highland adaptation, we crossed maize landraces from 108 highland and lowland sites of Mexico and South America with the inbred line B73 to produce F1 hybrids and grew them in both highland and lowland sites in Mexico. We identified thousands of genes with divergent expression between highland and lowland populations. Hundreds of these genes show patterns of convergent evolution between Mexico and South America. To dissect the genetic architecture of the divergent gene expression, we developed a novel allele-specific expression analysis pipeline to detect genes with divergent functional cis-regulatory variation between highland and lowland populations. We identified hundreds of genes with divergent cis-regulation between highland and lowland landrace alleles, with 20 in common between regions, further suggesting convergence in the genes underlying highland adaptation. Further analyses suggest multiple mechanisms contribute to this convergence. Our findings reveal a complex genetic architecture of cis-regulatory alleles underlying adaptation to highlands in maize. Although the vast majority of evolutionary changes associated with highland adaptation were region-specific, our findings highlight an important role for convergence at the gene expression and gene regulation levels as well.
Enhanced capillary pumping using open-channel capillary trees with integrated paper pads
Authors: Tokihiro Jodie C. , Tu Wan-chen , Berthier Jean , Lee Jing J. , Dostie Ashley M. , Khor Jian Wei , Eakman Madeleine , Theberge Ashleigh B. , Berthier Erwin 
Published: July 2022

ABSTRACTThe search for efficient capillary pumping has led to two main directions for investigation: first, assembly of capillary channels to provide high capillary pressures, and second, imbibition in absorbing fibers or paper pads. In the case of open microfluidics (i.e., channels where the top boundary of the fluid is in contact with air instead of a solid wall), the coupling between capillary channels and paper pads unites the two approaches and provides enhanced capillary pumping. In this work, we investigate the coupling of capillary trees— networks of channels mimicking the branches of a tree—with paper pads placed at the extremities of the channels, mimicking the small capillary networks of leaves. It is shown that high velocities and flow rates (7 mm/s or 13.1 µL/s) for more than 30 seconds using 50% (v/v) isopropyl alcohol, which has a 3-fold increase in viscosity in comparison to water; 6.5 mm/s or 12.1 µL/s for more than 55 seconds with pentanol, which has an 3.75-fold increase in viscosity in comparison to water; >3.5 mm/s or 6.5 µL/s for more than 150 seconds with nonanol, which has an 11-fold increase in viscosity in comparison to water) can be reached in the root channel, enabling higher sustained flow rates than that of capillary trees alone.
ACtivE: Assembly and CRISPR-targeted in vivo Editing for Yeast Genome Engineering Using Minimum Reagents and Time
Authors: Malcı Koray , Jonguitud-Borrego Nestor , van der Straten Hugo , Puodžiūnaitė Urtė , Johnston Emily J. , Rosser Susan J. , Rios-Solis Leonardo 
Published: July 2022

ABSTRACTAmong the numerous genetic tools developed for yeast, CRISPR/Cas system has been a widely used genome editing method thanks to its sophistication. However, CRISPR methods for yeast generally rely on pre-assembled DNAs and extra cloning steps to deliver gRNA, Cas protein, and donor DNA. These laborious steps might hinder its usefulness. Here, we propose a convenient, rapid, standardizable CRISPR method, named Assembly and CRISPR-targeted in vivo Editing (ACtivE), which only relies on in vivo assembly of linear DNA fragments for both plasmid and donor DNA construction. Thus, depending on the user’s need, these parts can be easily selected and combined from a repository, serving as a toolkit for rapid genome editing without any expensive reagent. The toolkit contains verified linear DNA fragments, which are easy to store, share and transport at room temperature, drastically reducing expensive shipping costs and assembly time. After optimizing this technique, eight ARS-close loci in the yeast genome were also characterized in terms of integration and gene expression efficiencies and the impacts of the disruptions of these regions on cell fitness. The flexibility and multiplexing capacity of the ACtivE were shown by constructing β-carotene pathway. In only a few days, > 80% integration efficiency for single gene integration and > 50% integration efficiency for triplex integration were achieved from scratch without using in vitro DNA assembly methods, restriction enzymes, or extra cloning steps. This study presents a standardizable method to be readily employed to accelerate yeast genome engineering and provides well-defined genomic location alternatives for yeast synthetic biology and metabolic engineering purposes.
Extended compartmental model for modeling COVID-19 epidemic in Slovenia
Authors: Fošnarič Miha , Kamenšek Tina , Gros Jerneja Žganec , Žibert Janez 
Published: July 2022

AbstractIn the absence of a systematic approach to epidemiological modeling in Slovenia, various isolated mathematical epidemiological models emerged shortly after the outbreak of the COVID-19 epidemic. We present an epidemiological model adapted to the COVID-19 situation in Slovenia. The standard SEIR model was extended to distinguish between age groups, symptomatic or asymptomatic disease progression, and vaccinated or unvaccinated populations. Evaluation of the model forecasts for 2021 showed the expected behavior of epidemiological modeling: our model adequately predicts the situation up to 4 weeks in advance; the changes in epidemiologic dynamics due to the emergence of a new viral variant in the population or the introduction of new interventions cannot be predicted by the model, but when the new situation is incorporated into the model, the forecasts are again reliable. Comparison with ensemble forecasts for 2022 within the European Covid-19 Forecast Hub showed better performance of our model, which can be explained by a model architecture better adapted to the situation in Slovenia, in particular a refined structure for vaccination, and better parameter tuning enabled by the more comprehensive data for Slovenia. Our model proved to be flexible, agile, and, despite the limitations of its compartmental structure, heterogeneous enough to provide reasonable and prompt short-term forecasts and possible scenarios for various public health strategies. The model has been fully operational on a daily basis since April 2020, served as one of the models for decision-making during the COVID-19 epidemic in Slovenia, and is part of the European Covid-19 Forecast Hub.
Highly multiplexed selection of RNA aptamers against a small molecule library
Authors: Townshend Brent , Kaplan Matias , Smolke Christina D. 
Published: July 2022

AbstractApplications of synthetic biology spanning human health, industrial bioproduction, and ecosystem monitoring often require small molecule sensing capabilities, typically in the form of genetically encoded small molecule biosensors. Critical to the deployment of greater numbers of these systems are methods that support the rapid development of such biosensors against a broad range of small molecule targets. Here, we use a previously developed method for selection of RNA biosensors against unmodified small molecules (DRIVER) to perform a selection against a densely multiplexed mixture of small molecules, representative of those employed in high-throughput drug screening. Using a mixture of 5,120 target compounds randomly sampled from a large diversity drug screening library, we performed a 95-round selection and then analyzed the enriched RNA biosensor library using next generation sequencing (NGS). From our analysis, we identified RNA biosensors with at least 2-fold change in signal in the presence of at least 217 distinct target compounds with sensitivities down to 25 nM. Although many of these biosensors respond to multiple targets, clustering analysis indicated at least 150 different small-molecule sensing patterns. We also built a classifier that was able to predict whether the biosensors would respond to a new compound with an average precision of 0.82. Since the target compound library was designed to be representative of larger diversity compound libraries, we expect that the described approach can be used with similar compound libraries to identify aptamers against other small molecules with a similar success rate. The new RNA biosensors (or their component aptamers) described in this work can be further optimized and used in applications such as biosensing, gene control, or enzyme evolution. In addition, the data presented here provide an expanded compendium of new RNA aptamers compared to the 82 small molecule RNA aptamers published in the literature, allowing further bioinformatic analyses of the general classes of small molecules for which RNA aptamers can be found.
Behavioral rhythms are bad predictors of general organismal rhythmicity
Authors: Sören Häfker N. , Holcik Laurenz , Vadiwala Karim , Beets Isabel , Mat Audrey M. , Stockinger Alexander W. , Hammer Stefan , Schoofs Liliane , Raible Florian , Tessmar-Raible Kristin 
Published: July 2022

ABSTRACTThe circadian clock controls behavior and metabolism in various organisms. However, the exact timing and strength of rhythmic phenotypes can vary significantly between individuals of the same species. This is highly relevant for the rhythmically complex marine environments where organismal rhythmic diversity likely permits the occupation of different microenvironments. When investigating circadian locomotor behavior ofPlatynereis dumerilii,a model system for marine molecular chronobiology, we found strain-specific, high variability between individual worms. The individual patterns were reproducibly maintained for several weeks independent of basic culture conditions, such as population density or feeding. A diel head transcriptome comparison of behaviorally rhythmic versus arrhythmic wildtype worms showed that 24h cycling of core circadian clock transcripts is identical between both behavioral phenotypes. While behaviorally arrhythmic worms showed a similar total number of cycling transcripts compared to their behaviorally rhythmic counterparts, the annotation categories of their transcripts, however, differed substantially. Consistent with their locomotor phenotype, behaviorally rhythmic worms exhibit an enrichment of cycling transcripts related to neuronal/behavioral processes. In contrast, behaviorally arrhythmic worms showed significantly increased diel cycling for metabolism- and physiology-related transcripts. Phenotype-specific cycling of distinct matrix metalloproteinase transcripts, encoding extracellular enzymes that modulate synaptic circuit function and neuropeptide signaling, like pigment dispersing factor (PDF), prompted us to functionally investigatePlatynereis pdf. Differing from its role inDrosophila,loss ofpdfimpacts on overall activity levels, but shows only indirect effects on rhythmicity. Our results show that individuals arrhythmic in a given process can show increased rhythmicity in others. Across thePlatynereispopulation, variations of this exist as a reproducible continuum. We hypothesize that such diel rhythm breadth is an important biodiversity resource enabling the species to quickly adapt to heterogeneous marine environments and potentially also to the effects of climate change, which is however endangered with shrinking population sizes and hence diversity.
West Nile virus and Usutu virus in wild birds from Rescue Centers, a post-mortem monitoring study from Central Italy
Authors: Giglia Giuseppe , Mencattelli Giulia , Lepri Elvio , Agliani Gianfilippo , Gobbi Marco , Gröne Andrea , van den Brand Judith M. A. , Savini Giovanni , Mandara Maria Teresa 
Published: July 2022

AbstractWest Nile virus (WNV) and Usutu virus (USUV) are mosquito-borne flaviviruses causing world-wide numerous cases in animals and humans. In Italy, both viruses have been associated with neurological diseases in humans and wild birds. Wild bird rescue centers where support in emergency and care of diseased animals are provided, are potential significant hot spots for avian infection surveillance, as recognized in the Italian Integrate National Surveillance Plan for Arboviruses. Here we report the results of a post-mortem active monitoring study conducted from November 2017 to October 2020 on animals hosted in five wild bird rescue centers of Central Italy. Five hundred seventy-six (n = 576) wild birds were tested by real-time polymerase chain reaction (RT-PCR) for the presence of WNV or USUV RNA fragments. No birds tested positive for USUV RNA (n = 0; 0.00 %). Evidence of WNV RNA (Ct value = 34.36) was found in one bird (n = 1; 0.17 %), an adult little grebe (Tachybaptus ruficollis subsp. ruficollis), that tested WNV positive on December 2019 and died due to traumatic injuries. The main pathological findings consisted in mild CD3+ lymphocytic tubulo-interstitial nephritis, meningoencephalitis, and cardiomyocytes loss and interstitial oedema of the heart. This study highlights the strategic role of wildlife rescue centers in monitoring both the introduction and circulation of avian emerging zoonotic diseases. Also, the presence of WNV during the cold season evidences the possible role of birds in overwintering mechanisms in the Italian territory and requires further investigations.
Evaluation of acaricidal activity of lithium-chloride against Tetranychus urticae (Acari: Tetranychidae)
Authors: Solti Izabella , Kolics Éva , Keszthelyi Sándor , Bacsi Zsuzsanna , Staszny Ádám , Nagy Erzsébet , Taller János , Mátyás Kinga , Kolics Balázs 
Published: July 2022

AbstractTetranychus urticae is a severe threat and a major source of yield loss in some agricultural and horticultural crops. Control is greatly complicated due to the hidden lifestyle of the species. In addition to its direct damage, it is considered a vector for several viruses. The number of active substances used against it is limited, and the development of resistance means that sustainable control is not achieved. Therefore, there is a continuous need for new active substances. Lithium salts have been shown to be a promising alternative to control Varroa destructor, an apicultural mite pest. Therefore, in the present study, we investigated whether the contact efficacy of lithium chloride extends to other agricultural mite pests, such as the two-spotted spider mite. In the present pilot study, we report for the first time that the efficacy of lithium chloride extends to the two-spotted spider mite, showing 100% mortality at concentrations of 5.52 M, 2.76 M, and 1.38 M. It is to note, however, that the experiments did not cover residue and practical application aspects, and further extensive studies are needed in this area to clarify the relevance of the practical sub-classification.
A vast world of viroid-like circular RNAs revealed by mining metatranscriptomes
Authors: Lee Benjamin D. , Neri Uri , Roux Simon , Wolf Yuri I. , Camargo Antonio Pedro , Krupovic Mart ,   RNA Virus Discovery Consortium, Simmonds Peter , Kyrpides Nikos , Gophna Uri , Dolja Valerian V. , Koonin Eugene V. 
Published: July 2022

SummaryViroids and viroid-like agents are unique, minimal RNA replicators that typically encode no proteins and hijack cellular enzymes for their genome replication. As the extent and diversity of viroid-like agents are poorly understood, we developed a computational pipeline to identify viroid-like covalently closed circular (ccc) RNAs and applied it to 5,131 global metatranscriptomes and 1,344 plant transcriptomes. The search resulted in 11,420 viroid-like, ribozyme-containing cccRNAs spanning 4,409 species-level clusters, which is a five-fold increase compared to the previously known set of viroids and viroid-like RNA agents. Within this diverse collection, we identified numerous putative novel viroids, satellite RNAs, retrozymes, and ribozylike viruses. We also found previously unknown ribozyme combinations and unusual ribozymes within the cccRNAs. Self-cleaving ribozymes were identified in both RNA strands of ambiviruses and some mito-like viruses as well as in capsid-encoding satellite virus-like cccRNAs. The broad presence of viroid-like cccRNAs in diverse transcriptomes and ecosystems implies that their host range is not limited to plants, and matches between viroid-like cccRNAs and CRISPR spacers suggest that some of them might replicate in prokaryotes.
Site-specific Halogenation of Peptides and Proteins using engineered Halogenase Enzymes
Authors: Sana Barindra , Ke Ding , Yen Li Eunice Hui , Ho Timothy , Seayad Jayasree , Duong Hung A , Ghadessy Farid J 
Published: July 2022

AbstractWe demonstrate novel in vitro halogenation of peptides by halogenase enzymes, and identify the (G/S)GW motif (HaloTryp Tag) as a preferred substrate. We further derive PyrH halogenase mutants showing improved halogenation of the HaloTryp Tag, both as a free peptide and when genetically fused to model proteins.
Understanding the Z-generation learner for contemporary teaching in Nigerian universities
Authors: Nwajiuba Chinyere Augusta , Onyeneke Robert Ugochukwu 
Published: July 2022

PurposeThis study investigated preferred learning and teaching styles of the Z-generation learners using Nigerian universities as a case.Design/methodology/approachThe visual, aural, read/write and kinesthetic (VARK) learning style model and the teaching method instrument were administered to 133 students' from private and public universities in Southeast Nigeria, and data collected were subjected to descriptive statistics and multivariate probit regression.FindingsThe students' preferred learning styles were auditory (90.2%), visual (83.5%), tactile (82.7%) and social interpersonal (73.7%). The findings indicate high preference for lecture with discussion among students while the least preferred teaching style was peer tutoring. Gender, programme of study, parents' marital status, students' socioeconomic and type of university showed different significant levels of interaction with learning style preference.Practical implicationsThe results suggest that contemporary university teachers teach concepts using audio–visual media tools and lecture method combined with discussions to enhance students’ learning experiences.Originality/valueDespite the numerous studies on learning and teaching styles preference among generations, the authors have not had until now any data examining the learning and teaching style preference of the Z-generation learner in the Nigerian context.
Service inclusion for tourists with disabilities: scale development and validation
Authors: Awan Maheen Iqbal , Shamim Amjad , Saleem Muhammad Shoaib , Gill Shahbaz Shabbir 
Published: July 2022

Purpose
The purpose of this study is to develop a scale for measuring service inclusion for tourists with disabilities in tourism and hospitality services. Transformative service research serves as the basis for the conceptualization and dimensionality.

Design/methodology/approach
To develop and purify the items as well as develop dimensions, standard scale development procedures were applied. Two studies were undertaken. In Study 1, the factorial structure of the service inclusion was constructed and confirmed using exploratory and confirmatory factor analysis. In Study 2, the field study was conducted to validate the scale.

Findings
The study developed a new scale for measuring service inclusion. The results show that service inclusion is a higher-order construct with four dimensions, namely, enabling opportunity, offering choice, relieving suffering and fostering happiness. Furthermore, service inclusion has a significant effect on tourists’ well-being perception, which results in more favorable behavioral responses. The newly constructed scale is declared as valid and reliable by the study that examined it for nomological validity by examining the relationship between service inclusion and tourists’ perceptions of their well-being.

Originality/value
To the best of the authors’ knowledge, this study is the first to develop measurement scale for service inclusion in the tourism and hospitality industry. The scale is proven as reliable and valid and is well suitable for measuring service inclusion for tourists with physical disabilities. It has potential to use for other relevant service contexts.