bluuebunny/crossref_metadata_2025_split huggingface dataset:
Susceptibility status of larvalAedes aegyptimosquitoes in Saudi Arabia
Authors: Al Nazawi Ashwaq M , Ashall Simon , Weetman David 
Published: December 2020

AbstractVector control programs worldwide are facing the challenge of mosquitoes becoming resistant to available insecticides. Larviciding is a crucial preventative measure for dengue control but data on insecticide resistance of larvalAe. aegyptiin the Middle Eastern Region are limited. This study assesses the susceptibility status ofAe. aegypticollected from the two most important dengue foci in Saudi Arabia, Jeddah and Makkah, to important chemical and biological larvicides; the organophosphate temephos andBacillus thuringiensis israelensis,Bti). Whilst worldwide, and particularly in Latin America, high-level resistance to temephos is common, Jeddah and Makkah populations exhibited full susceptibility to both temephos andBti.These data suggest each can be considered by vector control programs for preventative dengue control in the region, as part of temporal rotations or spatial mosaics to manage insecticide resistance.
Exp2Ipynb: A general machine-learning workflow for the analysis of promoter libraries
Authors: Liebal Ulf W. , Köbbing Sebastian , Blank Lars M. 
Published: December 2020

AbstractStrain engineering in biotechnology modifies metabolic pathways in microorganisms to overproduce target metabolites. To modify metabolic pathway activity in bacteria, gene expression is an effective and easy manipulated process, specifically the promoter sequence recognized by sigma factors. Promoter libraries are generated to scan the expression activity of different promoter sequences and to identify sequence positions that predict activity. To maximize information retrieval, a well-designed experimental setup is required. We present a computational workflow to analyse promoter libraries; by applying this workflow to seven libraries, we aim to identify critical design principles. The workflow is based on a Python Jupyter Notebook and covers the following steps: (i) statistical sequence analysis, (ii) sequence-input to expression-output predictions, (iii) estimator performance evaluation, and (iv) new sequence prediction with defined activity. The workflow can process multiple promoter libraries, across species or reporter proteins, and classify or regress expression activity. The strongest predictions in the sample libraries were achieved when the promoters in the library were recognized by a single sigma factor and a unique reporter system. A tradeoff between sample size and sequence diversity reduces prediction quality, and we present a relationship to estimate the minimum sample size. The workflow guides the user through analysis and machine-learning training, is open source and easily adaptable to include alternative machine-learning strategies and to process sequence libraries from other expression-related problems. The workflow is a contribution to increase insight to the growing application of high-throughput experiments and provides support for efficient strain engineering.AvailabilityFreely available on GitHub:https://qithub.com/iAMB-RWTH-Aachen/Exp2Ipynband licensed under the terms of GPLv3.Contactulf.liebal@rwth-aachen.deSupplementary informationSupplementary data available in the Git folder.
Widespread introgression across a phylogeny of 155Drosophilagenomes
Authors: Suvorov Anton , Kim Bernard Y. , Wang Jeremy , Armstrong Ellie E. , Peede David , D’Agostino Emmanuel R. R. , Price Donald K. , Wadell Peter , Lang Michael , Courtier-Orgogozo Virginie , David Jean R. , Petrov Dmitri , Matute Daniel R. , Schrider Daniel R. , Comeault Aaron A. 
Published: December 2020

ABSTRACTGenome-scale sequence data have invigorated the study of hybridization and introgression, particularly in animals. However, outside of a few notable cases, we lack systematic tests for introgression at a larger phylogenetic scale across entire clades. Here we leverage 155 genome assemblies, from 149 species, to generate a fossil-calibrated phylogeny and conduct multilocus tests for introgression across nine monophyletic radiations within the genusDrosophila. Using complementary phylogenomic approaches, we identify widespread introgression across the evolutionary history ofDrosophila. Mapping gene-tree discordance onto the phylogeny revealed that both ancient and recent introgression has occurred across most of the nine clades that we examined. Our results provide the first evidence of introgression occurring across the evolutionary history ofDrosophilaand highlight the need to continue to study the evolutionary consequences of hybridization and introgression in this genus and across the Tree of Life.
OpenTree: A Python package for Accessing and Analyzing data from the Open Tree of Life
Authors: McTavish Emily Jane , Sanchez Reyes Luna Luisa , Holder Mark T. 
Published: December 2020

AbstractThe Open Tree of Life project constructs a comprehensive, dynamic and digitally-available tree of life by synthesizing published phylogenetic trees along with taxonomic data. Open Tree of Life provides web-service application programming interfaces (APIs) to make the tree estimate, unified taxonomy, and input phylogenetic data available to anyone. Here, we describe the python packageopentree, which provides a user friendly python wrapper for these APIs and a set of scripts and tutorials for straightforward downstream data analyses. We demonstrate the utility of these tools by generating an estimate of the phylogenetic relationships of all bird families, and by capturing a phylogenetic estimate for all taxa observed at the University of California Merced Vernal Pools and Grassland Reserve.
Multispectral Fingerprinting Resolves Dynamics of Nanomaterial Trafficking in Primary Endothelial Cells
Authors: Gravely Mitchell , Roxbury Daniel 
Published: December 2020

AbstractIntracellular vesicle trafficking involves a complex series of biological pathways used to sort, recycle, and degrade extracellular components, including engineered nanomaterials which gain cellular entryviaactive endocytic processes. A recent emphasis on routes of nanomaterial uptake has established key physicochemical properties which direct certain mechanisms, yet relatively few studies have identified their effect on intracellular trafficking processes past entry and initial subcellular localization. Here, we developed and applied an approach where single-walled carbon nanotubes (SWCNTs) play a dual role - that of an engineered nanomaterial (ENM) undergoing intracellular processing, in addition to functioning as the signal transduction element reporting these events in individual cells with single organelle resolution. We used the unique optical properties exhibited by non-covalent hybrids of single-stranded DNA and SWCNTs (DNA-SWCNTs) to report the progression of intracellular processing eventsviatwo orthogonal hyperspectral imaging approaches of near-infrared (NIR) fluorescence and resonance Raman scattering. A positive correlation between fluorescence and G-band intensities was uncovered within single cells, while exciton energy transfer and eventual aggregation of DNA-SWCNTs were observed to scale with increasing time after internalization. These were confirmed to be consequences of intracellular processes using pharmacological inhibitors of endosomal maturation, which suppressed spectral changes through two distinct mechanisms. An analysis pipeline was developed to colocalize and deconvolute the fluorescence and Raman spectra of subcellular regions of interest (ROIs), allowing for single-chirality component spectra to be obtained with sub-micron spatial resolution. This approach uncovered a complex relationship between DNA-SWCNT concentration, fluorescence intensity, environmental transformations, and irreversible aggregation resulting from the temporal evolution of trafficking events. Finally, a spectral clustering analysis was applied to delineate the dynamic sequence of processes into four distinct populations, allowing stages of the intracellular trafficking process to be identified by the multispectral fingerprint of encapsulated DNA-SWCNTs.TOC Graphic
Comparative Genomics of Three Novel Lytic Jumbo Bacteriophages InfectingStaphylococcus aureus
Authors: Korn Abby M. , Hillhouse Andrew E. , Sun Lichang , Gill Jason J. 
Published: December 2020

AbstractThe majority of previously describedStaphylococcus aureusbacteriophages belong to three major groups: P68-likePodoviridae, Twort-like or K-likeMyoviridae,and a more diverse group of temperateSiphoviridae. Here we present three novelS. aureus“jumbo” phages: MarsHill, Madawaska, and Machias. These phages were isolated from swine production environments in the United States and represent a novel clade ofS. aureus Myoviridaethat is largely unrelated to other knownS. aureusphages. The average genome size for these phages is ~269 kb with each genome encoding ~263 predicted protein-coding genes. Phage genome organization and content is most similar to known jumbo phages ofBacillus, including AR9 and vB_BpuM-BpSp. All three phages possess genes encoding complete viral and non-viral RNA polymerases, multiple homing endonucleases, and a retron-like reverse transcriptase. Like AR9, all of these phages are presumed to have uracil-substituted DNA which interferes with DNA sequencing. These phages are also able to transduce host plasmids, which is significant as these phages were found circulating in swine production environments and can also infect humanS. aureusisolates.Importance of workThis study describes the comparative genomics of three novelS. aureusjumbo phages: MarsHill, Madawaska, and Machias. These threeS. aureus Myoviridaerepresent a new class ofS. aureusphage that have not been described previously. These phages have presumably hypermodified DNA which inhibits sequencing by several different common platforms. Therefore, not only are these phages an exciting new type ofS. aureusphage, they also represent potential genomic diversity that has been missed due to the limitations of standard sequencing techniques. The data and methods presented in this study could be useful for an audience far beyond those working inS. aureusphage biology. This work is original and has not been submitted for publication in any other journal.
Aging and MPTP-sensitivity depend on molecular and ultrastructural signatures of astroglia and microglia in mice substantia nigra
Authors: Abhilash PL , Bharti Upasna , Rashmi Santhosh Kumar , Philip Mariamma , Raju T. R. , Kutty Bindu M. , Chandrasekhar Sagar B.K. , Alladi Phalguni Anand 
Published: December 2020

ABSTRACTBoth astroglia and microglia show region-specific distribution in CNS and often maladapt to age-associated alterations within their niche. Studies on autopsied substantia nigra (SN) of Parkinson’s disease (PD) patients and experimental models propose gliosis as a trigger for neuronal loss. Epidemiological studies propose an ethnic bias in PD prevalence, since Caucasians are more susceptible than non-whites. Similarly, different mice strains are variably sensitive to MPTP. We had earlier likened divergent MPTP-sensitivity of C57BL/6J and CD-1 mice with differential susceptibility to PD, based on the numbers of SN neurons.Here, we examined whether the variability was incumbent to inter-strain differences in glial features of male C57BL/6J and CD-1 mice. Stereological counts showed relatively more microglia and fewer astrocytes in the SN of normal C57BL/6J mice, suggesting persistence of an immune-vigilant state. MPTP-induced microgliosis and astrogliosis in both strains, suggests their involvement in pathogenesis. ELISA of pro-inflammatory cytokines in the ventral-midbrain revealed augmentation of TNF-α and IL-6 at middle-age in both strains that reduced at old-age, suggesting middle-age as a critical, inflamm-aging associated time-point. TNF-α levels were high in C57BL/6J, through aging and post-MPTP; while IL-6 and IL-1β were upregulated at old-age. CD-1 had higher levels of anti-inflammatory cytokine TGF-β. MPTP-challenge caused upregulation of enzymes MAO-A, MAO-B and iNOS in both strains. Post-MPTP enhancement in fractalkine and hemeoxygenase-1; may be neuron-associated compensatory signals. Ultrastructural observations of elongated astroglial/microglial mitochondria vis-à-vis the shrunken ones in neurons, suggest a scale-up of their functions with neurotoxic consequences. Thus, astroglia and microglia modulate aging and PD-susceptibility.HighlightsSubstantia nigra of C57BL/6J and CD-1 show no baseline differences in glial numbersBoth mice show age and MPTP-induced gliosis in the substantia nigra pars compactaCD-1 nigra has lower levels of pro- and higher levels of anti-inflammatory cytokinesTilt of balance between pro- and anti-inflammatory cytokines begins at middle ageAstrocytes and microglia show elongated mitochondria and intact ER upon MPTP-injection
Human Erbb2-induced Erk Activity Robustly Stimulates Cycling and Functional Remodeling of Rat and Human Cardiomyocytes
Authors: Strash Nicholas , DeLuca Sophia , Janer Carattini Geovanni L. , Heo Soon Chul , Gorsuch Ryne , Bursac Nenad 
Published: December 2020

AbstractMultiple mitogenic pathways capable of promoting mammalian cardiomyocyte (CM) proliferation have been identified as potential candidates for functional heart repair following myocardial infarction. However, it is unclear whether the effects of these mitogens are species-specific and how they directly compare in the same cardiac setting. Here, we examined how CM-specific lentiviral expression of various candidate mitogens affects human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) and neonatal rat ventricular myocytes (NRVMs)in vitro. In 2D-cultured CMs from both species, and in highly mature 3D-engineered cardiac tissues generated from NRVMs, a constitutively-active mutant form of the human gene Erbb2 (cahErbb2) was the most potent tested mitogen. Persistent expression of cahErbb2 induced CM proliferation, sarcomere loss, and remodeling of tissue structure and function, which were attenuated by small molecule inhibitors of Erk signaling. These results suggest transient activation of Erbb2/Erk axis in cardiomyocytes as a potential strategy for regenerative heart repair.
Widespread premature transcription termination ofArabidopsis thalianaNLR genes by the spen protein FPA
Authors: Parker Matthew T. , Knop Katarzyna , Zacharaki Vasiliki , Sherwood Anna V. , Tome Daniel , Yu Xuhong , Martin Pascal , Beynon Jim , Michaels Scott , Barton Geoffrey J. , Simpson Gordon G. 
Published: December 2020

AbstractGenes involved in disease resistance are some of the fastest evolving and most diverse components of genomes. Large numbers ofnucleotide-binding,leucine-rich repeatreceptor (NLR) genes are found in plant genomes and are required for disease resistance. However, NLRs can trigger autoimmunity, disrupt beneficial microbiota or reduce fitness. It is therefore crucial to understand how NLRs are controlled. Here we show that the RNA-binding protein FPA mediates widespread premature cleavage and polyadenylation of NLR transcripts, thereby controlling their functional expression and impacting immunity. Using long-read Nanopore direct RNA sequencing, we resolved the complexity of NLR transcript processing and gene annotation. Our results uncover a co-transcriptional layer of NLR control with implications for understanding the regulatory and evolutionary dynamics of NLRs in the immune responses of plants.
Nigratine as first-in-class dual inhibitor of necroptosis and ferroptosis regulated cell death
Authors: Delehouzé Claire , Comte Arnaud , Hauteville Marcelle , Goekjian Peter , Dimanche-Boitrel Marie-Thérèse , Rousselot Morgane , Bach Stéphane 
Published: December 2020

AbstractNigratine (also known as 6E11), a natural flavanone derivative, was characterized as highly specific non-ATP competitive inhibitor of RIPK1 kinase, one of the key component of necroptotic cell death signaling. We show here that nigratine inhibited both necroptosis (induced by Tumor Necrosis Factor-α) and ferroptosis (induced by glutamate, erastin or RSL3 small chemical compounds) with EC50in the µM range. Altogether, the data obtained showed that nigratine is the first-in-class dual inhibitor of necroptosis and ferroptosis cell death routes and opened new therapeutic avenues for treating complex necrosis-related diseases.
Stretch-activated ion channels identified in the touch-sensitive structures of carnivorous Droseraceae plants
Authors: Procko Carl , Murthy Swetha E , Keenan William T , Reza Mousavi Seyed Ali , Dabi Tsegaye , Coombs Adam , Procko Erik , Baird Lisa , Patapoutian Ardem , Chory Joanne 
Published: December 2020

AbstractIn response to touch, some carnivorous plants such as the Venus flytrap have evolved spectacular movements to capture animals for nutrient acquisition. However, the molecules that confer this sensitivity remain unknown. We used comparative transcriptomics to show that expression of three genes encoding homologs of the MscS-Like (MSL) and OSCA/TMEM63 family of mechanosensitive ion channels are localized to touch-sensitive trigger hairs of Venus flytrap. We focus here on the candidate with the most enriched expression in trigger hairs, the MSL homolog FLYCATCHER1 (FLYC1). We show thatFLYC1transcripts are localized to mechanosensory cells within the trigger hair, transfecting FLYC1 induces chloride-permeable stretch-activated currents in naïve cells, and transcripts coding for FLYC1 homologs are expressed in touch-sensing cells of Cape sundew, a related carnivorous plant of the Droseraceae family. Our data suggest that the mechanism of prey recognition in carnivorous Droseraceae evolved by co-opting ancestral mechanosensitive ion channels to sense touch.
Palmitoylation of KChIP3 controls baseline mucin secretion
Authors: Cantero-Recasens G , Burballa C , Duran M , Brouwers N , Malhotra V 
Published: December 2020

AbstractBaseline mucin secretion (BMS) is independent of external agonists and controlled by a small calcium binding protein named KChIP3. KChIP3-hosting mucin granules are not released until intracellular cytosolic calcium oscillations reach a threshold, KChIP3 binds calcium and detaches from granules, allowing their fusion to plasma membrane. Loss of KChIP3 or blocking its membrane attachment causes mucin hypersecretion. How is KChIP3 recruited to mucin granules? We show here that zDHHC (aspartate-histidine-histidine-cysteine motif in a cysteine-rich, zinc finger–like domain) S-acyl-transferase dependent palmitoylation modulates binding of KChIP3 to mucin granules thereby affecting mucin secretion. We have found that inhibiting zDHHC-mediated palmitoylation in differentiated HT29-18N2, which express the Golgi-localized zDHHC3 and zDHHC4, releases KChIP3 from mucin granules and increases baseline mucin secretion. Mutation of the palmitoylation sites in KChIP3 (Cysteines 122 and 123 to Alanine) quantitatively reduces its attachment to mucin granules. Expression of KChIP3-WT in HT29-18N2 cell lines stably depleted of KChIP3 inhibits mucin secretion, whereas expression of non-palmitoylated KChIP3 (KChIP3-AA) only partially rescues the effect of KChIP3 depletion and the cells maintain higher levels of baseline secretion compared to KChIP3-WT cells. Altogether, our data suggest that zDHHC3 or zDHHC4-dependent palmitoylation is involved in KChIP3 recruitment to mucin granules to control the baseline mucin secretion.
Development of the destination food image scale (DFIS) and examination of measurement invariance by gender
Authors: Görür Hakan , Güzeller Cem Oktay 
Published: December 2020

PurposeThe main purpose of this study is to create a reliable and valid scale to assess the destination food image perceived by the tourists regarding the food in Turkey within the cognitive and affective image component framework. In line with this purpose, both scale development and scale adaptation studies are conducted, and measurement invariance of the scale for gender is analyzed.Design/methodology/approachThis study uses the survey model among quantitative research methods. Scale development processes are used to assess the cognitive image; the construct validity is analyzed with exploratory factor analysis (n = 328), confirmatory factor analysis (n = 425) and convergent and discriminant validity. Scale adaptation processes are followed to assess the affective image, and construct validity is tested with confirmatory factor analysis (n = 425). The reliability of both scales is investigated with Cronbach's alpha. Cochran–Mantel–Haenszel (CMH) analysis is conducted for measurement invariance for gender.FindingsConstruct validity and reliability provided the desired values in all processes. Measurement invariance results proved that the scale does not change according to genders.Research limitations/implicationsThe data obtained in this study have geographical limitations, and the data represent tourists visiting Antalya, an important tourism destination in Turkey.Practical implicationsThe scale will provide concrete information about the destination food image and help practitioners to test the model and develop future strategies for the destination.Originality/valueThis study presents an integrated approach to understanding the destination food image and expands theoretical and empirical evidence by creating a scale that measures both cognitive and affective image component. Scale-invariant shows that there is no item bias for analyzed gender and contributes to generalizability.
The link between HIWPs and well-being at work: the mediating role of trust
Authors: Uribetxebarria Urtzi , Gago Mónica , Legarra Maite , Elorza Unai 
Published: December 2020

PurposeThis paper examines the extent to which investment in human capital (HC) influences employee well-being, focusing on companies in the Basque Country in Northern Spain. Specifically, it analyzes the effects of worker perceptions of high-involvement work system (HIWS) on job satisfaction (JS) and affective commitment (AC), directly and through the mediating role of trust in management. This trust mediating role was also explored by analyzing the isolated effects of high-involvement work processes (power, information, reward and knowledge [PIRK] enhancing practices) on JS and AC.Design/methodology/approachThe structural equation modeling (SEM) approach was used on a sample of 2,199 employees from 425 organizations working in different industries. As the study was performed at the organizational level, aggregation was conducted first.FindingsThe findings revealed that trust partially mediated the relationship between HIWS and JS, although AC was directly predicted by the system. In contrast, a trust mediating role was confirmed in the relationship between all PIRK processes, JS and AC.Originality/valueThis study highlights the “hinge” role of trust in linking high-involvement work practices (HIWPs) as an approach to assess HC in organizations and well-being at work. It further conceptualizes HIWS via a PIRK model and operationalizes it through systemic and dimensional approach.