bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of a field-sprayed antibiotic on bee foraging behavior and pollination in pear orchards
Authors: Avila Laura , McCullough Christopher , Schiffer Annie , Moreno JoMari , Ganjur Neha , Ofenloch Zachary , DuPont Tianna , Nottingham Louis , Gerardo Nicole M. , Brosi Berry J. 
Published: February 2023

AbstractBroadcast spraying of antibiotics in crops is widely used for controlling bacterial plant pathogens. The effects of antibiotics on non-target (and especially beneficial) organisms in cropping systems, however, are not well studied. Pollinators are of particular concern because in pear and apple crops, antibiotics for controlling fire blight (Erwinia amylovora) are sprayed during bloom, likely exposing pollinators. This is especially relevant as laboratory evidence suggests that antibiotics could have sublethal effects on bee foraging behavior and colony health. But to our knowledge these potential impacts have not been studied in field settings. Here, we compared the effects of two fire blight control methods, a single spray of an antibiotic (oxytetracycline) and a biological antagonist (Aureobasidium pullulans), on honey bee (Apis mellifera) foraging, pollination, and fruit set in pear orchards. Complementing these field assessments, we conducted laboratory experiments to examine the effects of these treatments on locomotion and foraging behavior of the bumble bee species,Bombus vosnesenskii. We found that honey bees visited fewer flowers and foraged longer on each flower in orchards sprayed with antibiotics than with biological product, but there were no differences in pollination and seed set. The pear cultivars we worked in, however, can self-pollinate. In the lab, we found that feeding on high doses of either the antibiotic or the biological antagonist reduced bumble bee foraging behavior relative to controls. The limited impact of antibiotics on pear pollination observed in this study suggest that antibiotics pose a low economic risk to pear growers, especially for self-compatible cultivars. Still, crops with higher pollinator dependence may be more affected by reductions in pollinator visitation. Future studies should examine the impacts of multiple antibiotic sprays within a season, which are common during warm springs, and their long-term health impacts on both individual bees and colonies.HighlightsAntibiotics are sprayed on many crops to control plant bacterial pathogens.The impacts of antibiotics on beneficial organisms in agriculture are unknown.We studied antibiotic impacts on bee behavior and pollination function in pears.Bees exposed to antibiotics visit fewer flowers and this could impact bee fitness.Despite decreased bee visitation, we did not detect a reduction in crop pollination.Graphical Abstract
The genome of the toxic invasive speciesHeracleum sosnowskyicarries an increased number of genes despite absence of recent whole-genome duplications
Authors: Schelkunov MI , Shtratnikova VYu , Klepikova AV , Makarenko MS , Omelchenko DO , Novikova LA , Obukhova EN , Bogdanov VP , Penin AA , Logacheva MD 
Published: February 2023

AbstractHeracleum sosnowskyi, belonging to a group of giant hogweeds, is a plant with large effects on ecosystems and human health. It is an invasive species that contributes to the deterioration of grassland ecosystems. The ability ofH. sosnowskyito produce linear furanocoumarins (FCs), photosensitizing compounds, makes it very dangerous. At the same time, linear FCs are compounds with high pharmaceutical value that are used in skin disease therapies. Despite this high importance, it has not been the focus of genetic and genomic studies. Here, we report a chromosome-scale assembly of the Sosnowsky’s hogweed genome. Genomic analysis revealed an unusually high number of genes (55 206) in the hogweed genome, in contrast to the 25-35 thousand found in most plants. However, we did not find any traces of recent whole genome duplications not shared with its confamiliar,Daucus carota(carrot), which has approximately thirty thousand genes. The analysis of the genomic proximity of duplicated genes indicates tandem duplications as a main reason for this increase. We performed a genome-wide search of the genes of the FC biosynthesis pathway and their expression in aboveground plant parts. Using a combination of expression data and phylogenetic analysis, we found candidate genes for psoralen synthase and experimentally showed the activity of one of them using a heterologous yeast expression system. These findings expand our knowledge on the evolution of gene space in plants and lay a foundation for further analysis of hogweed as an invasive plant and as a source of FCs.
Sampling bias and the robustness of ecological metrics for plant–damage-type association networks: Comment
Authors: Schachat Sandra R. 
Published: February 2023

AbstractBipartite network metrics, which link taxa at two trophic levels, are notoriously biased when sampling is incomplete or uneven (Blüthgen et al., 2008; Dormann and Blüthgen, 2017; Fründ et al., 2016). Yet a new contribution (Swain et al., 2023, henceforth SEA) claims the opposite: that bipartite network metrics are minimally sensitive to incomplete sampling and, in fact, perform better at low sample sizes than traditional richness metrics. Here I show that SEA achieved this extraordinary finding by abandoning accepted practices, including practices from the authors’ previous papers.
Escherichia coliaggregates mediated by native or synthetic adhesins exhibit both core and adhesin-specific transcriptional responses
Authors: Chekli Yankel , Stevick Rebecca J. , Kornobis Etienne , Briolat Valérie , Ghigo Jean-Marc , Beloin Christophe 
Published: February 2023

AbstractBacteria can rapidly tune their physiology and metabolism to adapt to environmental fluctuations. In particular, they can adapt their lifestyle to the close proximity of other bacteria or presence of different surfaces. However, whether these interactions trigger transcriptomic responses is poorly understood. We used a specific set up ofE. colistrains expressing native or synthetic adhesins mediating bacterial aggregation to study the transcriptomic changes of aggregated compared to non-aggregated bacteria. Our results show that following aggregation, bacteria exhibit a core response independent of the adhesin type, with differential expression of 56.9% of the coding genome, including genes involved in stress response and anaerobic lifestyle. Moreover, when aggregates were formed via a naturally expressedE. coliadhesin (Antigen 43), the transcriptomic response of the bacteria was more exaggerated compared to aggregates formed via a synthetic adhesin. This suggests that the response to aggregation induced by nativeE. coliadhesins could have been finely tuned during bacterial evolution. Our study therefore provides insights on the effect of self-interaction in bacteria and allows a better understanding of why bacterial aggregates exhibit increased stress tolerance.ImportanceFormation of bacterial aggregates has an important role in both clinical and ecological contexts. Although these structures have been previously shown to be more resistant to stressful conditions, the genetic basis of this stress tolerance associated with the aggregate lifestyle is poorly understood. Surface sensing mediated by different adhesins can result in varying changes on bacterial physiology. However, whether adhesin-adhesin interactions as well as the type of adhesin mediating aggregation affects bacterial cell physiology is unknown. By sequencing the transcriptomes of aggregated and non-aggregated cells expressing native or synthetic adhesins, we characterized the effects of aggregation and adhesin type onE. coliphysiology.
Structural genomic variations and their effects on phenotypes inPopulus
Authors: Porth Ilga , Goessen Roos , Heinze Berthold 
Published: February 2023

AbstractDNA copy numbers have recently emerged as an important new marker system. In the absence of a contiguous reference genome, alternative detection systems such as the comparative hybridization method have been used to detect copy number variations (CNVs). With the advent of chromosome-level resolved reference genomes based on the incorporation of long-read sequencing and powerful bioinformatics pipelines, comprehensive detection of all structural variations (SVs) in the poplar genome is now within reach. Gene CNVs and their inheritance are important because they can cause dosage effects in phenotypic variations. These are potent genetic markers that should be considered in complex trait variation such as growth and adaptation in poplar. SVs such as CNVs could be used in future genomic selection studies for poplar, especially in cases when heterosis increases hybrid performance (hybrid vigor). This Chapter reports recent findings on SVs in natural populations ofPopulusspp. as well as on artificially induced SVs in poplar to understand their potential importance in generating a considerable amount of phenotypic improvement. The Chapter concludes with an outlook on the future implementation of knowledge on SVs in poplar crop breeding.
CXCR6 promotes dermal CD8+T cell survival and transition to long-term tissue residence
Authors: Heim Taylor A. , Lin Ziyan , Steele Maria M. , Mudianto Tenny , Lund Amanda W. 
Published: February 2023

AbstractTissue resident memory T cells (TRM) provide important protection against infection, and yet the interstitial signals necessary for their formation and persistence remain incompletely understood. Here we show that antigen-dependent induction of the chemokine receptor, CXCR6, is a conserved requirement for TRMformation in peripheral tissue after viral infection. CXCR6 was dispensable for the early accumulation of antigen-specific CD8+T cells in skin and did not restrain their exit. Single cell sequencing indicated that CXCR6-/-CD8+T cells were also competent to acquire a transcriptional program of residence but exhibited deficiency in multiple pathways that converged on survival and metabolic signals necessary for memory. As such, CXCR6-/-CD8+T cells exhibited increased rates of apoptosis relative to controls in the dermis, leading to inefficient TRMformation. CXCR6 expression may therefore represent a common mechanism across peripheral non-lymphoid tissues and inflammatory states that increases the probability of long-term residence.One Sentence SummaryCXCR6 promotes mechanisms of cellular adaptation to tissue infiltration that support local survival and the transition to tissue residence.
Epigenomic mapping in B-cell acute lymphoblastic leukemia identifies transcriptional regulators and noncoding variants promoting distinct chromatin architectures
Authors: Barnett Kelly R. , Mobley Robert J. , Diedrich Jonathan D. , Bergeron Brennan P. , Bhattarai Kashi Raj , Yang Wenjian , Crews Kristine R. , Manring Christopher S. , Jabbour Elias , Paietta Elisabeth , Litzow Mark R. , Kornblau Steven M. , Stock Wendy , Inaba Hiroto , Jeha Sima , Pui Ching-Hon , Mullighan Charles G. , Relling Mary V. , Yang Jun J. , Evans William E. , Savic Daniel 
Published: February 2023

SUMMARYB-cell lineage acute lymphoblastic leukemia (B-ALL) is comprised of diverse molecular subtypes and while transcriptional and DNA methylation profiling of B-ALL subtypes has been extensively examined, the accompanying chromatin landscape is not well characterized for many subtypes. We therefore mapped chromatin accessibility using ATAC-seq for 10 B-ALL molecular subtypes in primary ALL cells from 154 patients. Comparisons with B-cell progenitors identified candidate B-ALL cell-of-origin and AP-1-associatedcis-regulatory rewiring in B-ALL.Cis-regulatory rewiring promoted B-ALL-specific gene regulatory networks impacting oncogenic signaling pathways that perturb normal B-cell development. We also identified that over 20% of B-ALL accessible chromatin sites exhibit strong subtype enrichment, with transcription factor (TF) footprint profiling identifying candidate TFs that maintain subtype-specific chromatin architectures. Over 9000 inherited genetic variants were further uncovered that contribute to variability in chromatin accessibility among individual patient samples. Overall, our data suggest that distinct chromatin architectures are driven by diverse TFs and inherited genetic variants which promote unique gene regulatory networks that contribute to transcriptional differences among B-ALL subtypes.HIGHLIGHTSPro-B progenitor cells as the most common cell-of-origin for B-ALLAP-1 TF-associatedcis-regulatory rewiring in B-ALLSubtype-specific accessible chromatin signatures representing 20% of all B-ALL sitesRole for distinct TFs in promoting subtype-specific chromatin architecturesThousands of inherited genetic variants identified impacting chromatin state
BorderlinerpoBmutations transmit at the same rate as commonrpoBmutations in a tuberculosis cohort in Bangladesh
Authors: Lempens Pauline , Van Deun Armand , Aung Kya J.M. , Hossain Mohammad A. , Behruznia Mahboobeh , Decroo Tom , Rigouts Leen , de Jong Bouke C. , Meehan Conor J. 
Published: February 2023

AbstractThe spread of multidrug-resistant tuberculosis (MDR-TB) is a growing problem in many countries worldwide. Resistance to one of the primary first-line drugs, rifampicin, is caused by mutations in theMycobacterium tuberculosis rpoBgene. While some of these infrequent mutations show lower fitnessin vitrothan more common mutations, theirin vivofitness is currently unknown.We used a dataset of 394 whole genome sequenced MDR-TB isolates from Bangladesh, representing around 44% of notified MDR-TB cases over 6 years, to look at differences in transmission clustering between isolates with borderlinerpoBmutations and those with commonrpoBmutations. We found a relatively low percentage of transmission clustering in the dataset (34.8%) but no difference in clustering between different types ofrpoBmutations. Compensatory mutations inrpoA, rpoB, andrpoCwere associated with higher levels of transmission clustering as were lineages 2, 3, and 4 relative to lineage 1. Young people as well as patients with high sputum smear positive TB were more likely to be in a transmission cluster.Our findings show that although borderlinerpoBmutations have lowerin vitrogrowth potential this does not translate into lower transmission potential orin vivofitness. Proper detection of these mutations is crucial to ensure they do not go unnoticed and spread MDR-TB within communities.Data summaryWGS reads are available in the European Nucleotide Archive (PRJEB39569). In addition, WGS reads, as well as pDST and clinical data, are included in the ReSeqTB data platform and are accessible on registration athttps://platform.reseqtb.org/. Custom scripts for clustering are available athttps://github.com/conmeehan/pathophy.
Imaging the immune synapse: three-dimensional analysis of the immune synapse
Authors: Ruiz-Navarro Javier , Blázquez-Cucharero Sofía , Calvo Víctor , Izquierdo Manuel 
Published: February 2023

ABSTRACTT cell receptor (TCR) stimulation of T lymphocytes by antigen bound to the major histocompatibility complex (MHC) of an antigen-presenting cell (APC), together with the interaction of accessory molecules, induces the formation of the immunological synapse (IS), the convergence of secretion vesicles towards the centrosome, and the polarization of the centrosome to the IS. Upon IS formation, an initial increase in cortical filamentous actin (F-actin) at the IS takes place, followed by a decrease in F-actin density at the central region of the IS, which contains the secretory domain. These reversible, cortical actin cytoskeleton reorganization processes that characterize a mature IS occur during lytic granule secretion in cytotoxic T lymphocytes (CTL) and cytokine-containing vesicle secretion in T-helper (Th) lymphocytes. Besides, IS formation constitutes the basis of a signalling platform that integrates signals and coordinates molecular interactions that are necessary for an appropriate antigen-specific immune response. In this chapter we deal with the three-dimensional (3D) analysis of the synaptic interface architecture, as well as the analysis of the localization of different markers at the IS.
Metformin impairs trophoblast metabolism and differentiation in dose dependent manner
Authors: Nashif Sereen K. , Mahr Renee M. , Jena Snehalata , Jo Seokwon , Nelson Alisa B. , Sadowski Danielle , Crawford Peter A. , Puchalska Patrycja , Alejandro Emilyn U. , Gearhart Micah D. , Wernimont Sarah A. 
Published: February 2023

AbstractMetformin is a widely prescribed medication whose mechanism of action is not completely defined and whose role in gestational diabetes management remains controversial. In addition to increasing risks of fetal growth abnormalities and preeclampsia, gestational diabetes is associated with abnormalities in placental development including impairments in trophoblast differentiation. Given that metformin impacts cellular differentiation events in other systems, we assessed metformin’s impact on trophoblast metabolism and differentiation. Using established cell culture models of trophoblast differentiation, oxygen consumption rates and relative metabolite abundance were determined following 200 μM (therapeutic range) and 2000 μM (supra-therapeutic range) metformin treatment using Seahorse and mass-spectrometry approaches. While no differences in oxygen consumption rates or relative metabolite abundance were detected between vehicle and 200 μM metformin treated cells, 2000 μM metformin impaired oxidative metabolism and increased abundance of lactate and TCA cycle intermediates, α-ketoglutarate, succinate, and malate. Examining differentiation, treatment with 2000 μM, but not 200 μM metformin, impaired HCG production and expression of multiple trophoblast differentiation markers. Overall, this work suggests that supra-therapeutic concentrations of metformin impairs trophoblast metabolism and differentiation whereas metformin concentrations in the therapeutic range do not strongly impact these processes.
CUR(E)ating a New Approach to Study Fungal Effectors and Enhance Undergraduate Education through Authentic Research
Authors: Li Gengtan , McWilliams Mai , Rodrigues Matheus , Mearkle Benjamin , Jaafar Nader , Golla Vivek , Yu Houlin , Yang He , Ayhan Dilay Hazal , Allen Kelly , Martínez-Soto Domingo , Springer Amy , Ma Li-Jun 
Published: February 2023

ABSTRACTCourse-based Undergraduate Research Experiences (CUREs) integrate active, discovery-based learning into undergraduate curriculums, adding tremendous value to Biochemistry and Molecular Biology (BMB) education. There are multiple challenges in transforming a research project into a CURE, such as the readiness of students, the time commitment of the instructor, and the productivity of the research. In this article, we report a CURE course developed and offered in the University of Massachusetts Amherst BMB Department since 2018 that addresses these challenges. Our CURE focuses on fungal effectors which are proteins secreted by a destructive pathogenic fungusFusarium oxysporum, one of the top five most devastating plant pathogens. By studying this group of proteins, students are connected to real-world problems and participate in the search for potential solutions. A three-week “standard Bootcamp” is implemented to help students familiarize themselves with all basic techniques and boost their confidence. Next, molecular cloning, a versatile technique with modularity and repeatability, is used as the bedrock of the course. Our past five years of experience have confirmed that we have developed a novel and feasible CURE protocol. Measurable progress documented by students who took this course includes stimulated active learning and increased career trajectory to pursue hypothesis-based research to address societal needs. In addition, data generated through the course advance ongoing lab research. Collectively, we encourage the implementation of CURE among research-intensive faculty to provide a more inclusive research experience to all students, an important element in predicting career success.
Self-organizing actin networks drive sequential endocytic protein recruitment and vesicle release on synthetic lipid bilayers
Authors: Stoops Emily H. , Ferrin Michael A. , Jorgens Danielle M. , Drubin David G. 
Published: February 2023

AbstractForces generated by actin assembly assist membrane invagination during clathrin-mediated endocytosis (CME). The sequential recruitment of core endocytic proteins and regulatory proteins, and assembly of the actin network, are well documented in live cells and are highly conserved from yeasts to humans. However, understanding of CME protein self-organization, as well as the biochemical and mechanical principles that underlie actin’s role in CME, is lacking. Here, we show that supported lipid bilayers coated with purified yeast WASP, an endocytic actin assembly regulator, and incubated in cytoplasmic yeast extracts, recruit downstream endocytic proteins and assemble actin tails. Time-lapse imaging of WASP-coated bilayers revealed sequential recruitment of proteins from different endocytic modules, faithfully replicatingin vivobehavior. Reconstituted actin networks assemble in a WASP-dependent manner and deform lipid bilayers, as seen by electron microscopy. Time-lapse imaging revealed that vesicles are released from the lipid bilayers with a burst of actin assembly. Actin networks pushing on membranes have previously been reconstituted; here, we have reconstituted a biologically important variation of these actin networks that self-organize on bilayers and produce pulling forces sufficient to bud off membrane vesicles. We propose that actin-driven vesicle generation may represent an ancient evolutionary precursor to diverse vesicle forming processes adapted for a wide array of cellular environments and applications.Significance StatementActin filament assembly participates in many vesicle-forming processes. However, the underlying principles for how assembly is initiated and organized to effectively harness assembly forces remain elusive. To address this gap, we report a novel reconstitution of actin-driven vesicle release from supported lipid bilayers. Using real-time imaging, we observe sequential recruitment of endocytic proteins and, following a burst of actin assembly, vesicle release from bilayers. Given the absence of cargo or upstream endocytic regulatory proteins on the bilayers, and the participation of actin in many vesicle-forming processes, we posit that this mode of vesicle formation represents an early evolutionary precursor for multiple trafficking pathways. We expect that this assay will be of great use for future investigations of actin-mediated vesicle-forming processes.