bluuebunny/crossref_metadata_2025_split huggingface dataset:
A hitchhiker’s guide to Europe: mapping human-mediated dispersal of the invasive Japanese beetle
Authors: Borner Leyli , Martinetti Davide , Poggi Sylvain 
Published: October 2023

AbstractEarly detection of hitchhiking pests requires the identification of strategic entry points via transport. We propose a framework for achieving this in Europe using the Japanese beetle (Popillia japonica) as a case study. Human-mediated dispersal has been responsible for its introduction into several continents over the last century, including Europe where it is listed as a priority pest. Furthermore, interceptions far from the infested area confirm the risk of unintentional transport within continental Europe. Here, we analyse how three modes of transport - air, rail and road - connect the infested area to the rest of Europe. We ranked all European regions from most to least reachable from the infested area. We identified border regions and distant major cities that are readily reachable and observed differences between modes. We propose a composite reachability index combining the three modes, which provides a valuable tool for designing a continental surveillance strategy and prioritising highly reachable regions, as demonstrated by recent interceptions.Significance statementSpecies can be moved long distances by unintentional human transport. Such events can lead to their introduction into non-native areas where they can cause biological invasions. Using the case study of the Japanese beetle, a hitchhiker invasive insect, we propose a framework for identifying entry points for human-transported pests within Europe. We consider how the European infested area is connected to the rest of the continent by three modes of transport: air, rail and road. We propose a methodology that considers the three modes to identify potential entry points. This framework could assist authorities in designing surveillance strategies to achieve early detection of pests in Europe.
Chemotherapy activates inflammasomes to cause inflammation-associated bone loss
Authors: Wang Chun , Kaur Khushpreet , Xu Canxin , Abu-Amer Yousef , Mbalaviele Gabriel 
Published: October 2023

AbstractChemotherapy is a widely used treatment for a variety of solid and hematological malignancies. Despite its success in improving the survival rate of cancer patients, chemotherapy causes significant toxicity to multiple organs, including the skeleton, but the underlying mechanisms have yet to be elucidated. Using tumor-free mouse models, which are commonly used to assess direct off-target effects of anti-neoplastic therapies, we found that doxorubicin caused massive bone loss in wild-type mice, a phenotype associated with increased number of osteoclasts, leukopenia, elevated serum levels of danger-associated molecular patterns (DAMPs; e.g., cell-free DNA and ATP) and cytokines (e.g., IL-1β and IL-18). Accordingly, doxorubicin activated the absent in melanoma (AIM2) and NLR family pyrin domain containing 3 (NLRP3) inflammasomes in macrophages and neutrophils, causing inflammatory cell death pyroptosis and NETosis, which correlated with its leukopenic effects. Moreover, the effects of this chemotherapeutic agent on cytokine secretion, cell demise, and bone loss were attenuated to various extent in conditions of AIM2 and/or NLRP3 insufficiency. Thus, we found that inflammasomes are key players in bone loss caused by doxorubicin, a finding that may inspire the development of a tailored adjuvant therapy that preserves the quality of this tissue in patients treated with this class of drugs.
Staphyloccocus aureusbiofilm, in the absence of planktonic bacteria, produces factors that activate counterbalancing inflammatory and immune-suppressive genes in human monocytes
Authors: Bell Richard D , Cann E. Abrefi , Mishra Bikash , Valencia Melanie , Zhang Qiong , Yang Xu , Carli Alberto , Bostrom Mathias , Ivashkiv Lionel 
Published: October 2023

AbstractStaphyloccocus aureus(S. aureus) is a major bacterial pathogen in orthopedic periprosthetic joint infection (PJI).S. aureusforms biofilms that promote persistent infection by shielding bacteria from immune cells and inducing an antibiotic-resistant metabolic state. We developed an in vitro system to studyS. aureusbiofilm interactions with primary human monocytes in the absence of planktonic bacteria. In line with previous in vivo data,S. aureusbiofilm induced expression of inflammatory genes such asTNFandIL1B, and their anti-inflammatory counter-regulator IL-10.S. aureusbiofilm also activated expression of PD-1 ligands that suppress T cell function, and of IL-1RA that suppresses differentiation of protective Th17 cells. Gene induction did not require monocyte:biofilm contact and was mediated by a soluble factor(s) produced by biofilm-encased bacteria that was heat resistant and > 3 kD in size. Activation of suppressive genes by biofilm was sensitive to suppression by Jak inhibition. These results support an evolving paradigm that biofilm plays an active role in modulating immune responses, and suggest this occurs via production of a soluble vita-PAMP. Induction of T cell suppressive genes byS. aureusbiofilm provides insights into mechanisms that suppress T cell immunity in PJI, and suggest that anti-PD-1 therapy that is modeled on immune checkpoint blockade for tumors may be beneficial in PJI.
NAMERS: a purpose-built reference DNA sequence database to support applied eDNA metabarcoding
Authors: Westfall Kristen M. , Singer Gregory A. C. , Kaushal Muneesh , Gilmore Scott R. , Fahner Nicole , Hajibabaei Mehrdad , Abbott Cathryn L. 
Published: October 2023

ABSTRACTApplied eDNA metabarcoding is increasingly being used to generate actionable results to inform management decisions, regulations, or policy development. Because of these important downstream considerations, optimizing workflow elements is now essential to increasing standardization, efficiency, and confidence of metabarcoding results. Reference DNA sequences are critical workflow elements that currently lack consistent approaches to generating, curating, or publishing. Here we present a complete (mitochondrial genome and nuclear ribosomal DNA cistron) and high quality reference DNA sequence library for the freshwater fishes of British Columbia, Canada. This resource is published as the Novel Applied eDNA Metabarcoding Reference Sequences (NAMERS) repository (https://namers.ca), a user-friendly and interactive website for specialists and non-specialists alike to explore and generate custom reference libraries for taxa and genes of interest. We demonstrate the power of NAMERS to optimize applied eDNA metabarcoding workflows at the study design stage by analyzing the number of primer mismatches and resolution power of existing metabarcoding markers. To meet the increasing demand for actionable eDNA metabarcoding applications, NAMERS demonstrates that high quality curated genomic information is within a reasonable reach. It is timely to establish this framework as the new gold standard and coordinate our efforts to generate this type of reference data at scale.
Conservation of the ancestral function of GTSF1 in transposon silencing in the unicellular eukaryoteParamecium tetraurelia
Authors: Wang Chundi , Lv Liping , Solberg Therese , Wen Zhiwei , Zhang Haoyue , Gao Feng 
Published: October 2023

AbstractThe PIWI-interacting RNA (piRNA) pathway is crucial for transposon repression and the maintenance of genomic integrity. Gametocyte specific factor 1 (GTSF1), an indispensable auxiliary factor of PIWI, was recently shown to potentiate the catalytic activity of PIWI in many metazoans. Whether the requirement of GTSF1 extends to PIWI proteins beyond metazoans is unknown. In this study, we identified a homolog of GTSF1 in the unicellular eukaryoteParamecium tetraurelia(PtGTSF1) and found that its role as a PIWI-cofactor is conserved. PtGTSF1 interacts with PIWI (Ptiwi09) and Polycomb Repressive Complex 2 (PRC2) and is essential for PIWI-dependent DNA elimination of transposons during sexual development. PtGTSF1 is crucial for the degradation of PIWI-bound small RNAs recognizing the organism’s own genomic sequences. Without PtGTSF1, self-matching small RNAs are not degraded and results in an accumulation of H3K9me3 and H3K27me3, which disturbs transposon recognition and slows down their elimination. Our results demonstrate that the PIWI-GTSF1 interaction also exists in unicellular eukaryotes with the ancestral function of transposon silencing.
Response of soil bacteria to PUREX chemicals suggests biomarker utility and bioremediation potential
Authors: Podowski Justin C , Forrester Sara , Antonopoulos Dionysios A. , Steeb Jennifer L. , Kent Angela D. , Davis James J , Schabacker Daniel S. 
Published: October 2023

AbstractChemicals involved in plutonium uranium reduction extraction (PUREX) have the potential to be released from nuclear reprocessing facilities and accumulate in the environment. In order to understand how soil microbial communities respond to contamination by PUREX chemicals, we carried out a series of microcosm experiments, exposing chemically diverse soils to a range of concentrations of key chemicals used in the PUREX process. We tested 4 PUREX chemicals, and 5 soil types using 16S rRNA amplicon sequencing, determining that responses of microbial communities are dependent on the soil type in which they reside, and that tributyl phosphate exposure appears to generate the most reproducible and detectable shifts in microbial communities. We identified a number of key taxa that are consistently enriched in soils exposed to tributyl phosphate. These key taxa are either in the familyRhizobiaceaeor genusPseudomonas. The relative abundance of these key taxa is concentration dependent, and their abundance remains elevated at least 100 days post initial exposure. Using whole-shotgun metagenomic sequencing, we reconstructed the genomes of these key taxa and find a number of putative phosphotriesterase genes found only inRhizobiaceae. We find the abundance of phosphotriesterase genes is significantly higher in samples exposed to tributyl phosphate. These phosphotriesterase genes, which degrade tributyl phosphate into dibutyl phosphate and butanol, may serve as effective biomarkers for tributyl phosphate contaminated soil, as well as a method for future bioremediation.ImportanceNuclear materials reprocessing facilities have the capacity to release toxic chemicals during normal operations or accidents. This study examines the ways in which chemicals involved with nuclear materials reprocessing impact microorganisms in the soil. Our intention was to understand the consequences of the release of these chemicals on ecosystems that may surround these reprocessing facilities. We find soil microbial communities change in response to some chemicals but not others, and that tributyl phosphate appears to generate the most reproducible and detectable shifts in microbial communities. Microorganisms in the familyRhizobiaceaeincrease in abundance in response to the addition of tributyl phosphate, and an examination of the genomes of these microbes suggest they may be able to break down tributyl phosphate to access the phosphosphate present in this chemical. Overall, this work demonstrates that changes in soil microbial communities in response to contamination with chemicals from nuclear materials reprocessing facilities may be predictable, and these responses could be leveraged to remediate contamination.
Allele biased transcription factor binding across human brain regions gives mechanistic insight into eQTLs
Authors: Moyers Belle A. , Loupe Jacob M. , Felker Stephanie A. , Lawlor James M.J. , Anderson Ashlyn G. , Rodriguez-Nunez Ivan , Bunney William E. , Bunney Blynn G. , Cartagena Preston M. , Sequeira Adolfo , Watson Stanley J. , Akil Huda , Mendenhall Eric M. , Cooper Gregory M. , Myers Richard M. 
Published: October 2023

SummaryTranscription Factors (TFs) influence gene expression by facilitating or disrupting the formation of transcription initiation machinery at particular genomic loci. Because genomic localization of TFs is in part driven by TF recognition of DNA sequence, variation in TF binding sites can disrupt TF-DNA associations and affect gene regulation. To identify variants that impact TF binding in human brain tissues, we quantified allele bias for 93 TFs analyzed with ChIP-seq experiments of multiple structural brain regions from two donors. Using graph genomes constructed from phased genomic sequence data, we compared ChIP-seq signal between alleles at heterozygous variants within each tissue sample from each donor. Comparison of results from different brain regions within donors and the same regions between donors provided measures of allele bias reproducibility. We identified thousands of DNA variants that show reproducible bias in ChIP-seq for at least one TF. We found that alleles that are rarer in the general population were more likely than common alleles to exhibit large biases, and more frequently led to reduced TF binding. Combining ChIP-seq with RNA-seq, we identified TF-allele interaction biases with RNA bias in a phased allele linked to 6,709 eQTL variants identified in GTEx data, 3,309 of which were found in neural contexts. Our results provide insights into the effects of both common and rare variation on gene regulation in the brain. These findings can facilitate mechanistic understanding of cis-regulatory variation associated with biological traits, including disease.
Fabrication of Crescent Shaped Microparticles for Particle Templated Droplet Formation
Authors: Yang Yimin , Vagin Sergei I. , Rieger Bernhard , Destgeer Ghulam 
Published: October 2023

AbstractCrescent-shaped hydrogel microparticles have been shown to template uniform volume aqueous droplets upon simple mixing with aqueous and oil media for various bioassays. This emerging “lab on a particle” technique requires hydrogel particles with tunable material properties and dimensions. The crescent shape of the particles is attained by aqueous two-phase separation of polymers inside a spherical droplet followed by photopolymerization of the curable precursor. In this work, we have investigated the phase separation of photo-curable poly(ethylene glycol) diacrylate (PEGDA,Mw700) and dextran (Mw40,000) for tunable manufacturing of crescent-shaped particles. The particles’ morphology was precisely tuned by following a phase diagram, varying the UV intensity, and adjusting the flow rate ratio between the three streams, containing PEGDA, dextran, and oil, within a microfluidic droplet generation device. The fabricated particles with variable cavity sizes and outer diameters encapsulated uniform aqueous droplets upon mixing with a continuous oil phase. The particles were fluorescently labeled with red and blue emitting dyes at variable concentrations to produce six color-coded particles. The blue fluorescent dye showed a moderate response to the pH change from 1 to 7 in terms of an increase in emitted intensity. The fluorescently labeled particles were able to tolerate an extremely acidic solution (pH 1) but disintegrated within an extremely basic solution (pH 14). The particle-templated droplets were able to effectively retain the disintegrating particle and the fluorescent signal at pH 14, indicating completely segregated compartments.
Potential intrahospital dissemination ofPseudomonas aeruginosacarrying theblaIMP-1gene within a Tn7-like transposon
Authors: Zheng Lin , Wang Zixian , Guo Jingyi , Guan Jiayao , Li Quanliang , Lu Gejin , Jing Jie , Sun Shiwen , Sun Yang , Ji Xue , Jiang Bowen , Chen Ping , Yang Yanling , Zhu Lingwei , Guo Xuejun 
Published: October 2023

AbstractWe aimed to determine the molecular characteristics of carbapenem-resistantPseudomonas aeruginosa18081308 and 18083286 isolated from the urine and sputum of two Chinese patients respectively, and analyzed the formation mechanism of the genetic environment in which it carriesblaIMP-1. Bacterial genome sequencing was carried out on strains 18081308 and 18083286 to obtain their whole genome sequence. Average nucleotide identity (ANI) was used for their precise species identification. Serotyping and multilocus sequence typing were performed. Furthermore, the acquired resistance genes, and virulence factors of these strains were identified. The carbapenem-resistantP. aeruginosastrains isolated in the present study were of sequence type ST865 and serotype O6. They all carried the same virulence factors (PLC, ExoSTY) and resistance genes (aacC2,tmrB, andblaIMP-1). Tn6411, a Tn7-like transposon carryingblaIMP-1, was found in both strains. Detailed genetic dissection was applied to this transposon to display the genetic environment ofblaIMP-1. TheaacC2-tmrBregion remnant-Tn6411backbone was the original structure of this type of transposon. A Tn402-like type 1 integron (intl1-aac(6’)-II-blaIMP-1) was inserted into it and formed a stable structure, which was localized in the chromosome by TnsD for transmission withinP. aeruginosa; the original structure of Tn7-like transposon was localized on the plasmid by TnsE for horizontal transmission between bacterial species.The intrahospital dissemination ofP. aeruginosaST865 isolated in this study was episodic. TheblaIMP-1-carrying Tn7-like transposon might enhance their ability to survive under drug selection pressure and aggravate the difficulty in treating infections.
Genomic analyses of Asiatic Mouflon in Iran provide insights into the domestication and evolution of sheep
Authors: Wang Dong-Feng , Orozco-terWengel Pablo , Li Meng-Hua , Lv Feng-Hua 
Published: October 2023

AbstractBackgroundAsiatic mouflon (O. gmelini) consists of several subspecies mainly distributed in Armenia, southern Azerbaijan, Cyprus, northern, southern, and western regions of Iran, and eastern and central regions of Turkey nowadays. Genome analyses of Asiatic mouflon in Iran revealed that they could have diverged from the direct ancestor of domestic sheep, and showed genetic introgression into domestic sheep after domestication. However, the impact of the Asiatic mouflon subspecies in Iran on sheep domestication remains unclear.ResultsHere, we conducted a comprehensive population genomics analysis of Asiatic mouflons in Iran with 780 whole-genome sequences, 767 whole mitogenomes, and 239 Y chromosomes. Whole-genome sequence analyses revealed two subpopulations of the Asiatic mouflons in Iran:O. gmelini_2 limited in Kabudan andO. gmelini_1 over a wide geographic area. Phylogenetic analyses of the Asiatic mouflons in Iran based on uniparental variants revealed a monophyletic lineage with the mitochondrial haplogroups C+E, and clustered into a monophyletic with Y-chromosomal lineage HY2 of sheep. Additionally, introgression tests detected significant signals of genetic introgression fromO. gmelini_2 to four sheep populations (e.g., Garut, Garole, Bangladeshi, and Sumatra) in South and Southeast Asia. In the four sheep populations, selective tests and introgression signals revealed that the wild introgression could have contributed to their small body size and local adaptation to the hot and humid environments in the Indian Peninsula.ConclusionsOur results suggested that the maternal haplogroups C+E and paternal lineage HY2 could have originated from the Asiatic mouflon in Iran. Also, our findings provide new insights into sheep domestication and subsequent introgressions from wild ancestors to domestic populations.
40 Hz Light Flickering Promotes Sleep through Cortical Adenosine Signaling
Authors: He Yan , Zhou Xuzhao , Xu Tao , Wu Zhaofa , Guo Wei , Xu Xi , Liu Yuntao , Zhang Yi , Shang Huiping , Yao Zhimo , Li Zewen , Li Zhihui , Feng Tao , Zhang Shaomin , Cunha Rodrigo A. , Huang Zhili , Li Yulong , Cai Xiaohong , Qu Jia , Chen Jiang-Fan 
Published: October 2023

AbstractFlickering light stimulation has emerged as a promising non-invasive neuromodulation strategy to alleviate neuropsychiatric disorders. However, the lack of a neurochemical underpinning has hampered its therapeutic development. Here, we demonstrate that light flickering triggered an immediate and sustained increase (up to 3 hours after flickering) in extracellular adenosine levels in the primary visual cortex and other brain regions, as a function of light frequency, intensity, and wavelength, with maximal effects observed at 40 Hz frequency. We discovered cortical (glutamatergic and GABAergic) neurons, rather than astrocytes, as the cellular source, and intracellular adenosine generation from calcium influx-triggered, AMPK- associated energy metabolism pathways (but not SAM-transmethylation or salvage purine pathways) and adenosine efflux mediated by equilibrative nucleoside transporter-2 (ENT2) as the molecular pathway responsible for extracellular adenosine generation. Importantly, 40 Hz light flickering for 30 min enhanced sleep in mice in a frequency-dependent manner. This somnogenic effect was absent in mice lacking ENT2 but replicated by administering adenosine to the visual cortex. Brief 40 Hz light flickering also promoted sleep in children with insomnia by decreasing sleep onset latency, increasing total sleep time, and reducing waking after sleep onset. Collectively, our findings establish adenosine signaling via ENT2 as the neurochemical basis for 40 Hz flickering-induced sleep and unravel a novel and non-invasive treatment for insomnia, a condition that affects 20% of the world population.
Engineered blue-shifted melanopsins for subcellular optogenetics
Authors: Wijayaratna Dhanushan , Sacchetta Filippo , Pedraza Gonzalez Laura , Fanelli Francesca , Sugihara Tomohiro , Koyanagi Mitsumasa , Piyawardana Senuri , Ghotra Kiran , Thotamune Waruna , Terakita Akihisa , Olivucci Massimo , Karunarathne Ajith 
Published: October 2023

AbstractMelanopsin (MeOp) is a G protein-coupled Receptor (GPCR) family photopigment, expressed in intrinsically photosensitive retinal ganglion cells (ipRGCs) that display remarkable functional diversity. In addition to non-image-forming visual functions, MeOp also controls signaling underlying the retina development, circadian clock, mood, and behavior. MeOp is bistable, recycles retinal, and can function under low retinaldehyde availability. It also activates multiple G protein heterotrimers. Though MeOp could be a versatile optogenetic tool, its potential, especially its utility for subcellular signaling control, is hampered by the broader spectral sensitivity spanning the entire visible range. Here, we use a recently reportedin silicotechnology called Automatic Rhodopsin Modeling (ARM) to identify blue-shifting mutations of MeOp and, ultimately, allow for imaging biosensors with red light without activating the opsin. Accordingly, ARM was used to construct validated quantum mechanics/molecular mechanics (QM/MM) models for mouse MeOp (mMeOp) to search and optimize a set of mutants featuring a blue-shifted light absorption. We demonstrate that four mutants of such can be successfully expressed and display the required resistance to activation by red light; however, they are activated by yellow, green, and blue light. Localized subcellular optical activation of these mutants in macrophage cells showed localized PIP3 generation and cell migration. Further characterization showed that MeOp blue-shifted mutants are also bistable. Altogether, our data demonstrate the computer-aided engineering feasibility of opsins with desired spectral properties for subcellular optogenetic applications.