bluuebunny/crossref_metadata_2025_split huggingface dataset:
Public adherence to precautionary measures and preventive guidelines against COVID-19 in Sudan: An application of the Health Belief Model
Authors: Mehanna Azza , Mohammed Elhadi Yasir Ahmed , Lucero-Prisno Don Eliseo 
Published: December 2020

AbstractBackgroundCorona virus disease (COVID-19) is highly infectious disease caused by the novel corona virus (SARS-CoV-2). Several public health and social protective measures that may prevent or slow down the transmission of COVID-19 were introduced. However, these measures are unfortunately neglected or deliberately ignored by some individuals.MethodsWe did a cross sectional online based survey to identify possible factors influencing intention to adhere to precautionary measures and preventive guidelines against COVID-19 during lockdown periods in Sudan. The questionnaire was used to collect socio-demographic data of study participants, their health beliefs and intention regarding adherence to precautionary measures against COVID-19 based on the constructs of the Health Belief Model.ResultsTotal of 680 respondents completed and returned the online questionnaire. Significant predictors of intention to adhere to the precautionary measures against COVID-19 were gender (β =3.34, P <0.001), self-efficacy (β= 0.476, P<0.001), perceived benefits (β= 0.349, P<0.001) and perceived severity (β= 0.113, P=0.005). These factors explained 43% of the variance in respondents’ intention to adhere to COVID-19 precautionary measures. Participants who were female, confident in their ability to adhere to the protective measures when available, believing in the benefits of the protective measures against COVID-19 and perceiving that the disease could have serious consequences were more likely to be willing to adhere to the protective measures.ConclusionFemale respondents and respondents having higher self-efficacy, higher perceived benefits and higher perceived severity were more likely to be willing to adhere to the protective measures against COVID-19 in Sudan.
Digging behavior discrimination test to probe burrowing and exploratory digging in male and female mice
Authors: Pond Heather L. , Heller Abigail T. , Gural Brian M. , McKissick Olivia P. , Wilkinson Molly K. , Manzini M. Chiara 
Published: December 2020

AbstractDigging behavior is often used to test motor function and repetitive behaviors in mice. Different digging paradigms have been developed for behaviors related to anxiety and compulsion in mouse lines generated to recapitulate genetic mutations leading to psychiatric and neurological disorders. However, the interpretation of these tests has been confounded by the difficulty of determining the motivation behind digging in mice. Digging is a naturalistic mouse behavior, that can be focused toward different goals, i.e. foraging for food, burrowing for shelter, burying objects, or even for recreation as has been shown for dogs, ferrets, and human children. However, the interpretation of results from current testing protocols assumes the motivation behind the behavior often concluding that increased digging is a repetitive or compulsive behavior. We asked whether providing a choice between different types of digging activities would increase sensitivity to assess digging motivation. Here, we present a test to distinguish between burrowing and exploratory digging in mice. We found that mice prefer burrowing when the option is available. When food restriction was used to promote a switch from burrowing to exploration, males readily switched from burrowing to digging outside, while females did not. In addition, when we tested a model of intellectual disability and autism spectrum disorder that had shown inconsistent results in the marble burying test, theCc2d1aconditional knock-out mouse, we found greatly reduced burrowing only in males. Our findings indicate that digging is a nuanced motivated behavior and suggest that male and female rodents may perform it differently.Significance StatementDigging behavior is commonly assessed in mice to study features of neurodevelopmental, psychiatric and neurological disorder. However, existing digging assays fail to discriminate between types of digging complicating data interpretation. Here we present a modified digging behavior discrimination task that can produce sensitive results in 30 minutes with easy to gather measures, making it accessible to wide variety of labs and experimental paradigms.
Using Genetic Information to Improve the Prediction of Individual Food Choice: A Case Study of Alcoholic Beverages
Authors: Zhu Chen , Beatty Timothy , Zhao Qiran , Si Wei , Chen Qihui 
Published: December 2020

AbstractIndividual food choices and consumption are closely relating to one’s diet, nutrition, and health. Using the case of alcoholic beverages, this study extends the random-utility framework by incorporating genetic information into consumer demand models, and demonstrates the significant impact of genetic factors on individual food choice decisions in a novel way. Integrating individual-level responses of discrete choice experiments (DCE), genotyping data, and socioeconomic/demographic characteristics of 484 participants collected from face-to-face interviews in mainland China, we employ a machine learning-based classification (MLC) approach to identify and predict individual choices. We show that genetic factors are critical to explaining variations in both general drinking behavior and choices of particular products. We systematically compared the performance of traditional discrete choice models and MLC models without and with genetic factors. The MLC predictive model with both socio-demographic and genetic features yields the highest accuracy of 74.7% and AUC-ROC of 0.85. Our findings warrant further economic studies of human behaviors with the integration of genetic data.
The size of helical pitch is important for microtubule plus end dynamic instability
Authors: Liu Chenshu , Prahl Louis , He Yu , Wang Yan , Zhu Ruijun , Mao Yinghui 
Published: December 2020

ABSTRACTMicrotubule (MT) dynamic instability is a conserved phenomenon underlying essential cellular functions such as cell division, cell migration and intracellular transport, and is a key target of many chemotherapeutic agents. However, it remains unclear how the organization of tubulin dimers at the nanometer scale translates into dynamic instability as an emergent property at the micrometer scale. Tubulin dimers are organized into left-handed helical MT lattice, and most present-day MTs converge at a 1.5 dimer helical pitch that causes a seam in an otherwise symmetric helix. Because presently there are no experimental methods that can precisely manipulate tubulin subunit with sub-dimer resolution, the impact of helical pitch on dynamic instability remains unknown. Here by using stochastic simulations of microtubule assembly dynamics we demonstrate that helical pitch plays essential roles in MT plus end dynamic instability. By systematically altering helical pitch size, one half-dimer at a time, we found that a helical pitch as small as one half-dimer is sufficient to inhibit short-term MT length plateaus associated with diminishing GTP-tubulin cap. Notably, MT plus end dynamics quantitatively scale with the size of helical pitch, rather than being clustered by the presence or absence of helical symmetry. Microtubules with a 1.5 dimer helical pitch exhibit growth and shrinkage phases and undergo catastrophe and rescue similar to experimentally observed microtubules. Reducing helical pitch to 0 promotes rapid disassembly, while increasing it causes microtubules to undergo persistent growth, and it is the 1.5 dimer helical pitch that yields the highest percentage of MTs that undergo alternating growth and shrinkage without being totally disassembled. Finally, although the 1.5 dimer helical pitch is conserved among most present-day MTs, we find that other parameters, such as GTP hydrolysis rate, can partially compensate for changes in helical pitch. Together our results indicate that helical pitch is a determinant of MT plus end dynamic instability and that the evolutionarily conserved 1.5 dimer helical pitch promotes dynamic instability required for microtubule-dependent cellular functions.
Activity-Dependent Modulation of Synapse-Regulating Genes in Astrocytes
Authors: Farhy-Tselnicker I , Boisvert MM , Liu H , Dowling C , Erikson GA , Blanco-Suarez E , Farhy C , Shokhirev M , Ecker JR , Allen NJ 
Published: December 2020

SummaryAstrocytes regulate the formation and function of neuronal synapses via multiple signals, however, what controls regional and temporal expression of these signals during development is unknown. We determined the expression profile of astrocyte synapse-regulating genes in the developing mouse visual cortex, identifying astrocyte signals that show differential temporal and layer-enriched expression. These patterns are not intrinsic to astrocytes, but regulated by visually-evoked neuronal activity, as they are absent in mice lacking glutamate release from thalamocortical terminals. Consequently, synapses remain immature. Expression of synapse-regulating genes and synaptic development are also altered when astrocyte signaling is blunted by diminishing calcium release from astrocyte stores. Single nucleus RNA sequencing identified groups of astrocytic genes regulated by neuronal and astrocyte activity, and a cassette of genes that show layer-specific enrichment. Thus, the development of cortical circuits requires coordinated signaling between astrocytes and neurons, identifying astrocytes as a target to manipulate in neurodevelopmental disorders.
NMDA receptor–BK channel coupling regulates synaptic plasticity in the barrel cortex
Authors: Gómez Ricardo , Maglio Laura E. , Gonzalez-Hernandez Alberto J. , Rivero-Pérez Belinda , Bartolomé-Martín David , Giraldez Teresa 
Published: December 2020

SUMMARYPostsynaptic N-methyl-D-aspartate receptors (NMDARs) are crucial mediators of synaptic plasticity due to their ability to act as coincidence detectors of presynaptic and postsynaptic neuronal activity. However, NMDARs exist within the molecular context of a variety of postsynaptic signaling proteins, which can fine-tune their function. Here we describe a novel form of NMDAR suppression by large-conductance Ca2+- and voltage-gated K+(BK) channels in the basal dendrites of a subset of barrel cortex layer 5 pyramidal neurons. We show that NMDAR activation increases intracellular Ca2+in the vicinity of BK channels, thus activating K+efflux and strong negative feedback inhibition. We further show that neurons exhibiting such NMDAR–BK coupling serve as high-pass filters for incoming synaptic inputs, precluding the induction of spike-timing-dependent plasticity. Together, these data suggest that NMDAR-localized BK channels regulate synaptic integration and provide input-specific synaptic diversity to a thalamocortical circuit.
A genome-scale yeast library with inducible expression of individual genes
Authors: Arita Yuko , Kim Griffin , Li Zhijian , Friesen Helena , Turco Gina , Wang Rebecca Y. , Climie Dale , Usaj Matej , Hotz Manuel , Stoops Emily , Baryshnikova Anastasia , Boone Charles , Botstein David , Andrews Brenda J. , McIsaac R. Scott 
Published: December 2020

AbstractThe ability to switch a gene from off to on and monitor dynamic changes provides a powerful approach for probing gene function and elucidating causal regulatory relationships, including instances of feedback control. Here, we developed and characterized YETI (Yeast Estradiol strains with Titratable Induction), a collection in which 5,687 yeast genes are engineered for transcriptional inducibility with single-gene precision at their native loci and without plasmids. Each strain contains Synthetic Genetic Array (SGA) screening markers and a unique molecular barcode, enabling high-throughput yeast genetics. We characterized YETI using quantitative growth phenotyping and pooled BAR-seq screens, and we used a YETI allele to characterize the regulon ofROF1,showing that it is a transcriptional repressor. We observed that strains with inducible essential genes that have low native expression can often grow without inducer. Analysis of data from other eukaryotic and prokaryotic systems shows that low native expression is a critical variable that can bias promoter-perturbing screens, including CRISPRi. We engineered a second expression system, Z3EB42, that gives lower expression than Z3EV, a feature enabling both conditional activation and repression of lowly expressed essential genes that grow without inducer in the YETI library.
Detectability of biotin tags by LC-MS/MS
Authors: Nierves Lorenz , Lange Philipp F. 
Published: December 2020

ABSTRACTThe high affinity of biotin to streptavidin has made it one of the most widely used affinity tags in proteomics. Early methods used biotin for enrichment alone and mostly ignored the biotin labeled peptide. Recent advances in labeling led to an increase in biotinylation efficiency and shifted the interest to detection of the site of biotinylation. This increased confidence in identification and provides additional structural information yet it requires efficient release of the biotinylated protein/peptide and sensitive separation and detection of biotinylated peptides by LC-MS/MS. Despite its long use in affinity proteomics the effect of biotinylation on the chromatographic, ionization, and fragmentation behaviour and ultimate detection of peptides is not well understood. To address this we compare two commercially-available biotin labels EZ-Link Sulfo-NHS-Biotin and Sulfo-NHS-SS-Biotin, the latter one containing a labile linker to efficiently release biotin to determine the effects of peptide modification on peptide detection. We describe an increase of hydrophobicity and charge reduction with increasing number of biotin labels attached. Based on our data we recommend gradient optimization to account for more hydrophobic biotinylated peptides and include singly charged precursors to account for charge reduction by biotin.
A novel and effective Cre/lox-based genetic tool for repeated, targeted and markerless gene integration
Authors: Zhou Qinghua , Jiao Liangcheng , Li Wenjuan , Hu Zhiming , Li Yunchong , Zhang Houjin , Xu Li , Yan Yunjun 
Published: December 2020

AbstractThe unconventional yeastYarrowia lipolyticais extensively applied in bioproduction fields owing to its excellent metabolite and protein production ability. Nonetheless, utilization of this promising host is still restricted by limited availability of precise and effective gene integration tools. In this study, a novel and efficient genetic tool was developed for targeted, repeated, and markerless gene integration based on Cre/loxsite-specific recombination system. The developed tool required only a single selection marker and could completely excise all of the unnecessary sequences. A total of three plasmids were created and seven rounds of marker-free gene integration were examined inY. lipolytica. All the integration efficiencies remained above 90%, and analysis of protein production and growth characteristics of the engineered strains confirmed that genome modification via the novel genetic tool was feasible. Further work also confirmed the genetic tool was effective for integration of other genes, loci, and strains. Thus, this study significantly promotes the application of Cre/loxsystem and presents a powerful tool for genome engineering inY. lipolytica.Graphical abstractThe novel genetic tool comprised three plasmids, namely, Cre-Y1, Cre-Y2, and Cre-Y3. Cre-Y1 was introduced into the Upleu locus of Po1f, and then recombination between twolox71 sites could remove unnecessary plasmid elements and produce an initial strain harboring alox71 site. Subsequently, Cre-Y2 was integrated onto theleu2locus, forming a transitional strain with threeloxsites (lox71,lox66, and rclox66). Recombination reactions among these threeloxsites could excise unnecessary DNA fragments and retain alox72 site, an rclox66 site, and a target gene expression cassette in the genome. Similarly, integration of Cre-Y3 produced strains harboring two target gene expression cassettes. Consequently, repeated, targeted, and markerless gene integration could be efficiently realized following iterative integration of Cre-Y2 and Cre-Y3.HighlightsA powerful genetic tool was developed for targeted and markerless gene integrationThe genetic tool was effective for various genes, loci, and strainsOnly a single selection marker was adequate for repeated gene integrationAll of the useless and redundant sequences would be excisedAll integration efficiencies could remain above 90%
Rif2 protects Rap1-depleted telomeres from MRX-mediated degradation inSaccharomyces cerevisiae
Authors: Rosas Bringas Fernando R. , Stinus Sonia , de Zoeten Pien , Cohn Marita , Chang Michael 
Published: December 2020

AbstractRap1 is the main protein that binds double-stranded telomeric DNA inSaccharomyces cerevisiae. Examination of the telomere functions of Rap1 is complicated by the fact that it also acts as a transcriptional regulator of hundreds of genes and is encoded by an essential gene. In this study, we disrupt Rap1 telomere association by expressing a mutant telomerase RNA subunit (tlc1-tm) that introduces mutant telomeric repeats.tlc1-tmcells grow similar to wild-type cells, although depletion of Rap1 at telomeres causes defects in telomere length regulation and telomere capping. Rif2 is a protein normally recruited to telomeres by Rap1, but we show that Rif2 can still associate with Rap1-depletedtlc1-tmtelomeres, and that this association is required to inhibit telomere degradation by the MRX complex. We find that Rap1, Rif2, and the Ku complex work in parallel to prevent telomere degradation, and absence of all three at telomeres causes lethality. The partially redundant mechanisms may explain the rapid evolution of telomere components in budding yeast species.
Evidence for nutrient-dependent regulation of the COPII coat by O-GlcNAcylation
Authors: Bisnett Brittany J. , Condon Brett M. , Linhart Noah A. , Lamb Caitlin H. , Huynh Duc T. , Bai Jingyi , Smith Timothy J. , Hu Jimin , Georgiou George R. , Boyce Michael 
Published: December 2020

AbstractO-linked β-N-acetylglucosamine (O-GlcNAc) is a dynamic form of intracellular glycosylation common in animals, plants and other organisms. O-GlcNAcylation is essential in mammalian cells and is dysregulated in myriad human diseases, such as cancer, neurodegeneration and metabolic syndrome. Despite this pathophysiological significance, key aspects of O-GlcNAc signaling remain incompletely understood, including its impact on fundamental cell biological processes. Here, we investigate the role of O-GlcNAcylation in the coat protein II complex (COPII), a system universally conserved in eukaryotes that mediates anterograde vesicle trafficking from the endoplasmic reticulum. We identify new O-GlcNAcylation sites on Sec24C, Sec24D and Sec31A, core components of the COPII system, and provide evidence for potential nutrient-sensitive pathway regulation through site-specific glycosylation. Our work suggests a new connection between metabolism and trafficking through the conduit of COPII protein O-GlcNAcylation.
De novosynthesis of phosphatidylcholine is essential for the promastigote but not amastigote stage inLeishmania major
Authors: Moitra Samrat , Basu Somrita , Pawlowic Mattie , Hsu Fong-fu , Zhang Kai 
Published: December 2020

ABSTRACTPhosphatidylcholine (PC) is the most abundant type of phospholipids in eukaryotes constituting ~30% of total lipids inLeishmania. PC synthesis mainly occurs via the choline branch of the Kennedy pathway (choline ⇒ choline-phosphate ⇒ CDP-choline ⇒ PC) and the N-methylation of phosphatidylethanolamine (PE). In addition,Leishmaniaparasites can acquire PC and other lipids from the host or culture medium. In this study, we assessed the function and essentiality of choline ethanolamine phosphotransferase (CEPT) inLeishmania majorwhich is responsible for the final step of thede novosynthesis of PC and PE. Our data indicate that CEPT is localized in the endoplasmic reticulum and possesses the activity to generate PC from CDP-choline and diacylglycerol. Targeted deletion ofCEPTis only possible in the presence of an episomalCEPTgene in the promastigote stage ofL. major. These chromosomal null parasites require the episomal expression ofCEPTto survive in culture, confirming its essentiality during the promastigote stage. In contrast, duringin vivoinfection of BALB/c mice, these chromosomal null parasites appeared to lose the episomal copy ofCEPTwhile maintaining normal levels of virulence, replication and cellular PC. Therefore, while thede novosynthesis of PC/PE is indispensable for the proliferation of promastigotes, intracellular amastigotes appear to acquire most of their lipids through salvage and remodeling.
Cheese or cheese infusions – ecological traps for mosquitoes and spotted wing Drosophila
Authors: Peach Daniel , Almond Max , Ko Elton , Meraj Sanam , Gries Regine , Gries Gerhard 
Published: December 2020

AbstractWe tested the hypothesis that the “ecological trap” phenomenon (a mismatch between a habitat’s perceived attractiveness and its actual quality, resulting in a population sink) is exploitable for pest control. We selected mosquitoes as modal organisms, because selection of an oviposition site by adult female mosquitoes in response to its perceived attractiveness is of paramount importance for the development and survival of their larval offspring. In laboratory and/or field experiments, we show that (i) each of five cheese varieties tested (Raclette, Pecorino, Brie, Gruyere, Limburger) strongly attracts females of both the yellow fever mosquito,Aedes aegypti, and the common house mosquito,Cx. pipiens;(ii) cheese infusions, or headspace odorant extracts (HOEs) of cheese infusions, significantly affect oviposition choices byCx. pipiensandAe. aegypti, (iii) HOEs contain at least 13 odorants; (iv) in field settings, cheese infusions more effectively stimulate oviposition byCx. pipiensandCuliseta incidensthan bluegrass (Poasp.) infusions, and also capture (by drowning) the spotted wingDrosophila(SWD); (v) the microbe composition of home-made cheese infusions modulates oviposition choices by mosquitoes; and (vi) the type of cheese infusion coupled with its nutritional content strongly affects the survivorship of mosquito larvae. In combination, our data show that microbial metabolites associated with cheese and cheese infusions are both attractive to adult mosquitoes seeking hosts and oviposition sites, respectively, and are toxic to mosquito larvae. These microbes and their metabolites could thus be coopted for both the attract and the kill function of “attract & kill” mosquito control tactics. Implementation of customizable and non-conventional nutritional media, such as home-made cheese infusions, as microbe-based ecological traps presents a promising concept which exploits insect ecology for insect control.