bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabarcoding and ecological interaction networks for selecting candidate biological control agents
Authors: Ollivier Mélodie , Lesieur Vincent , Tavoillot Johannes , Bénetière Fanny , Tixier Marie-Stéphane , Martin Jean-François 
Published: May 2021

AbstractClassical biological control can be used to decrease the density of invasive species to below an acceptable ecological and economic threshold. Natural enemies specific to the invasive species are selected from its native range and released into the invaded range. This approach has drawbacks, despite the performance of specificity tests to ensure its safety, because the fundamental host range defined under controlled conditions does not represent the actual host rangein natura, and these tests omit indirect interactions within community.We focus onSonchus oleraceus(Asteraceae), a weed species originating from Western Palearctic that is invasive worldwide and notably in Australia. We explore how analyses of interaction network within its native range can be used to 1) inventory herbivores associated to the target plant, 2) characterize their ecological host ranges, and 3) guide the selection of candidate biocontrol agents considering interactions with species from higher trophic levels. Arthropods were collected from plant community sympatric toS. oleraceus, in three bioclimatic regions, and interactions were inferred by a combination of molecular and morphological approaches.The networks reconstructed were structured in several trophic levels from basal species (diversified plant community), to intermediate and top species (herbivorous arthropods and their natural enemies). The subnetwork centered onS. oleraceusrelated interactions contained 116 taxa and 213 interactions. We identified 47 herbivores feeding onS. oleraceus, 15 of which were specific to the target species (i.e. Generality value equal to 1). Some discrepancies with respect to published findings or conventional specificity tests suggested possible insufficient sampling effort for the recording of interactions or the existence of cryptic species. Among potential candidate agents, 6 exhibited interactions with natural enemies.Synthesis and applications:Adopting a network approach as prerequisite step of the CBC program can provide a rapid screening of potential agents to be tested in priority. Once ecological host range defined, we suggest that priority should be given to agent predated by a minimum species, and, when they exist, to an agent that possesses enemies from the most distant taxonomical group from those occurring in the range of introduction.
Bacteriostatic antibiotics promote the evolution of CRISPR-Cas immunity
Authors: Dimitriu Tatiana , Kurilovich Elena , Lapinska Urszula , Severinov Konstantin , Pagliara Stefano , Szczelkun Mark D. , Westra Edze R. 
Published: May 2021

AbstractPhage therapy can be used in combination with antibiotics to combat infections with bacterial pathogens1–3. However, bacteria can rapidly evolve phage resistance via receptor mutation, or using their CRISPR-Cas adaptive immune systems4, which insert short phage-derived sequences into CRISPR loci in the bacterial genome5to guide sequence-specific cleavage of cognate sequences6. Unlike CRISPR-Cas immunity, mutation of the phage receptor leads to attenuated virulence when the opportunistic pathogenPseudomonas aeruginosais infected with its phage DMS3vir7, which underscores the need to predict how phage resistance evolves under clinically relevant conditions. Here, using eight antibiotics with various modes of action, we show that bacteriostatic antibiotics (which inhibit cell growth without killing) specifically promote evolution of CRISPR-Cas immunity inP. aeruginosaby slowing down phage development and providing more time for cells to acquire phage-derived sequences and mount an immune response. Our data show that some antimicrobial treatments can contribute to the evolution of phage-resistant pathogens with high virulence.
Population structure and association mapping for hundred seed weight in mungbean minicore
Authors: Akhtar Muhammad Arslan , Aslam Muhammad , Schafleitner Roland , Ahsan Muhammad , Murtaza Ghulam 
Published: May 2021

AbstractMungbean is an important legume rich in protein and carbohydrates. It is cultivated mostly in south to south east Asia and east Africa. One of the important yield contributing traits in mungbean is 100 seed weight. Variation for this trait is available in the mungbean germplasm, and to facilitate improvement of this trait through breeding, genome-wide association mapping for 100 seed weight was carried out in the World Vegetable Center mungbean minicore collection. A total of 24,870 single nucleotide polymorphic markers were tested for association with 100 see weight in plants grown in Pakistan, Bangladesh, Myanmar and Taiwan and candidate loci associated with seed weight on chromosomes 1, 4, 6, 8 and 9 were identified. None of the QTLs was stable across all environments, but loci on chromosomes 4 and 8 were significant in Pakistan and Bangladesh and other loci on chromosome 8 were significantly associated in plants grown in Myanmar and Taiwan.
Immunomodulatory Therapy with Glatiramer Acetate Reduces Endoplasmic Reticulum Stress and Mitochondrial Dysfunction in Experimental Autoimmune Encephalomyelitis
Authors: Makar Tapas K. , Guda Poornachander R , Ray Sugata , Andhavarapu Sanketh , Nimmagadda Vamshi KC , Gerzanich Volodymyr , Simard Marc J , Bever Christopher T. 
Published: May 2021

AbstractEndoplasmic reticulum (ER) stress and mitochondrial dysfunction are found in lesions of multiple sclerosis (MS) and of experimental autoimmune encephalomyelitis (EAE), an animal model of MS, and may contribute to the neuronal loss that underlies permanent impairment. These pathological changes are due to the neuroinflammation that characterizes MS and the strong interplay between the ER and mitochondria. We investigated whether immunomodulatory drug glatiramer acetate (GA) can reduce these changes in the spinal cords of chronic EAE mice by using routine histology, immunostaining, and electron microscopy. EAE spinal cord tissue exhibited increased infiltration/inflammation (upregulation of proinflammatory cytokines), demyelination, mitochondrial dysfunction (increased fission, decreased fusion, and increased biogenesis), ER stress, downregulation of NAD+ dependent pathways, and increased neuronal death. GA reversed these pathological changes, suggesting that immunomodulating therapy can attenuate ER stress, mitochondrial dysfunction, apoptotic cell death, and demyelination in the CNS and increase NAD+ utilizing activities by suppressing neuroinflammation.
The Mediator tail module cooperates with proneural factors to determine fate identity in Glioblastoma
Authors: Ahmadi Moloud , MacLeod Graham , Rajakulendran Nishani , Kosic Milena , Yang Andy , Molaei Fatemeh , Lin Sichun , Steinhart Zachary , Park Nicole I. , Dirks Peter B. , Angers Stephane 
Published: May 2021

AbstractGlioblastoma stem cells (GSCs) exhibit latent neuronal lineage differentiation potential governed by the proneural transcription factor Achaete-scute homolog 1 (ASCL1) and harnessing and promoting terminal neuronal differentiation has been proposed as a novel therapeutic strategy. Here, using a genome-wide CRISPR suppressor screen we identified genes required for ASCL1-mediated neuronal differentiation. This approach revealed a specialized function of the Mediator complex tail module and of its subunits MED24 and MED25 for this process in GSCs, human fetal neural stem cells and pluripotent stem cells. We show that upon induction of neuronal differentiation MED25 is recruited to genomic loci co-occupied by ASCL1 to regulate neurogenic gene expression programs. MED24 and MED25 are sufficient to induce neuronal differentiation in GSC cultures and to mediate neuronal differentiation in multiple contexts. Collectively our data expand our understanding of the mechanisms underlying directed terminal neuronal differentiation in brain tumor stem cells and point to a unique function of the Mediator tail in neuronal reprogramming.
Haploinsufficiency of the essential gene RpS12 causes defects in erythropoiesis and hematopoietic stem cell maintenance
Authors: Folgado-Marco Virginia , Ames Kristina , Chuen Jacky , Gritsman Kira , Baker Nicholas E. 
Published: May 2021

AbstractRibosomal protein (Rp) gene haploinsufficiency can result in Diamond-Blackfan Anemia (DBA), characterized by defective erythropoiesis and skeletal defects. Some mouse Rp mutations recapitulate DBA phenotypes, although others lack erythropoietic or skeletal defects. We generated a conditional knockout mouse to partially deleteRpS12, which results in homozygous embryonic lethality.Rps12+/-mice have growth and morphological defects, pancytopenia and impaired erythropoiesis. A striking reduction in hematopoietic stem cells (HSCs) and progenitors in the bone marrow (BM) was associated with decreased ability to repopulate the blood system after competitive and non-competitive BM transplantation. The mutants exhibited loss of HSC quiescence, which was associated with ERK and MTOR activation and increased global translation in HSC and progenitors. Thus, RpS12 has a very strong requirement in maintaining HSC quiescence and function, in addition to erythropoiesis that is affected in DBA patients.
Convergence Assessment for Bayesian Phylogenetic Analysis using MCMC simulation
Authors: Fabreti Luiza Guimarães , Höhna Sebastian 
Published: May 2021

SummaryPosterior distributions are commonly approximated by samples produced from a Markov chain Monte Carlo (MCMC) simulation. Every MCMC simulation has to be checked for convergence, i.e., that sufficiently many samples have been obtained and that these samples indeed represent the true posterior distribution.Here we develop and test different approaches for convergence assessment in phylogenetics. We analytically derive a threshold for a minimum effective sample size (ESS) of 625. We observe that only the initial sequence estimator provides robust ESS estimates for common types of MCMC simulations (autocorrelated samples, adaptive MCMC, Metropolis-Coupled MCMC). We show that standard ESS computation can be applied to phylogenetic trees if the tree samples are converted into traces of absence/presence of splits.Convergence in distribution between replicated MCMC runs can be assessed with the Kolmogorov-Smirnov test. The commonly used potential scale reduction factor (PSRF) is biased when applied to skewed posterior distribution. Additionally, we analytically derive the expected difference between split frequencies (EDSF) and show that it depends on the true frequency of a split. Hence, the average standard deviation of split frequencies is too simplistic and the EDSF should be used instead to check for convergence in split frequencies.We implemented the methods described here in the open-source R package Convenience (https://github.com/lfabreti/convenience), which allows users to easily test for convergence using output from standard phylogenetic inference software.
Comparative meta-proteomic analysis for the identification of novel plasmodesmata proteins and regulatory cues
Authors: Kirk Philip , Amsbury Sam , German Liam , Gaudioso-Pedraza Rocio , Benitez-Alfonso Yoselin 
Published: May 2021

SummaryA major route for cell-to-cell signaling is via cell wall-embedded pores termed plasmodesmata (PD) forming the symplasm. PD regulate many aspects of plant development and responses to the environment however, our understanding of what factors affect their structure and permeability is limited. In this paper, a meta-analysis is presented as a tool for the identification of conditions affecting PD transport and in silico generation of PD proteomes for species of interest. The custom-built pipeline searches the whole genome for protein structural features and conserved domains identified on experimental proteomes and use it to predict PD candidates in 22 compatible plant species. Using the in silico proteome and microarray analysis, interactions between PD genes and conditions affecting PD function are identified. High salinity and osmotic stress affect a significant number of PD candidate genes and we provide evidence that these conditions regulate symplasmic transport of GFP. Using the pipeline, the in silico PD proteome for Medicago truncatula was generated, as an example of a plant in which experimental data is not available. The identification of a candidate receptor like protein was experimentally validated in M. truncatula transgenic roots expressing fluorescently tagged protein fusion. Together the results highlight the power of our newly designed tool in the identification of new factors and proteins influencing PD in diverse plant species.
Hierarchical Bayesian Integrated Model for Estimating Migratory Bird Harvest in Canada
Authors: Smith Adam C. , Villeneuve Thomas , Gendron Michel 
Published: May 2021

ABSTRACTThe Canadian Wildlife Service (CWS) requires reliable estimates of the harvest of migratory game birds, including waterfowl, to effectively manage populations of these hunted species. The National Harvest Survey is an annual survey of hunters who purchase Canada’s mandatory migratory game bird hunting permit, integrating information from a survey of hunting activity with information from a separate survey of species composition in the harvest. We use these survey data to estimate the number of birds harvested for each species, as well as hunting activity metrics such as the number of active hunters and days spent hunting. The analytical methods used to generate these estimates have not changed since the survey was first designed in the early 1970s. Here we describe a new hierarchical Bayesian integrated model, which replaces the series of ratio estimators that comprised the old model. We are now using this new model to generate estimates for migratory bird harvests as of the 2019-2020 hunting season, and to generate updated estimates for all earlier years. The hierarchical Bayesian model uses over-dispersed Poisson distributions to model mean hunter activity and harvest (zero inflated Poisson and zero truncated Poisson, respectively). It also includes multinomial distributions to model some key components including, variation in total harvest across periods of the hunting season, the species composition of the harvest within each of those periods, and the age and sex composition in the harvests of a given species. We estimated the parameters of the Poisson and the multinomial distributions for each year as random effects using first-difference time-series. This time-series component allows the model to share information across years and reduces the sensitivity of the estimates to annual sampling noise. The new model estimates are generally very similar to those from the old model, particularly for the species that occur most commonly in the harvest, and so the results do not suggest any major changes to harvest management decisions and regulations. However, estimates for all species from the new model are more precise and less susceptible to annual sampling error, particularly for species that occur less commonly in the harvest (e.g., sea ducks and other species of conservation concern). This new model, with its hierarchical Bayesian framework, will also facilitate future improvements and elaborations, allowing the incorporation of prior information from the rich literature and knowledge in game bird management and biology.
Reorganization of molecular networks associated with DNA methylation and changes in the rearing environments of the house wren (Troglodytes aedon)
Authors: vonHoldt Bridgett M. , Kartzinel Rebecca Y. , van Oers Kees , Verhoeven Koen J.F. , Ouyang Jenny 
Published: May 2021

AbstractEnvironmental change, such as increased rates of urbanization, can induce shifts in phenotypic plasticity with some individuals adapting to city life while others are displaced. A key trait that can facilitate adaptation is the degree at which animals respond to stress. This stress response has a heritable component and exhibits intra- and inter-individual variation. However, the mechanisms behind this variability and whether they might be responsible for adaptation to different environments are not known. Variation in DNA methylation can be a potential mechanism that mediates environmental effects on the stress response. We used an inter- and intra-environmental cross-foster experiment to analyze the contribution of DNA methylation to early-life phenotypic variation. We found that at hatching, urban house wren (Troglodytes aedon) offspring had increased methylation as compared to their rural counterparts, and observed plasticity in methylation as offspring aged, indicating developmental effects of the rearing environment on methylation. Differential methylation analyses showed that cellular respiration genes were differentially expressed at hatching and behavioral and metabolism genes were differentially expressed at fledgling. Lastly, hyper-methylation of a single gene (CNTNAP2) is associated with increased glucocorticoid levels. These differential methylation patterns linked to a specific physiological phenotype suggest that DNA methylation may be a mechanism by which individuals adapt to novel environments. Characterizing genetic and environmental influences on methylation is critical for understanding the role of epigenetic mechanisms in evolutionary adaptation.
Probing pathophysiology of extracellular cGAMP with substrate-selective ENPP1
Authors: Carozza Jacqueline A. , Cordova Anthony F. , AlSaif Yasmeen , Böhnert Volker , Skariah Gemini , Li Lingyin 
Published: May 2021

AbstractThe biology of the immune second messenger cGAMP depends on its cellular localization. cGAMP, which is synthesized in response to cytosolic double-stranded DNA, also exists in the extracellular space as a paracrine immunotransmitter that enhances the anticancer immune response. However, the role of extracellular cGAMP is unexplored outside of cancer due to a lack of tools to systemically manipulate it. The extracellular enzyme ENPP1, the only known hydrolase of cGAMP, is a promising target. However, because ENPP1 also degrades extracellular ATP, using genetic knockouts of ENPP1 to study extracellular cGAMP leads to confounding effects. Here we report the H362A point mutation in ENPP1, the dominant cGAMP hydrolase, which selectively abolishes ENPP1’s ability to degrade cGAMP, while retaining activity toward other substrates. H362 is not necessary for binding cGAMP or the catalytically-essential zinc atoms but instead supports the in-line reaction geometry. H362 is evolutionarily conserved down to bacteria, suggesting an ancient origin for extracellular cGAMP biology. Enpp1H362A mice do not display the systemic calcification seen in Enpp1-/- mice, highlighting the substrate-specific phenotype of ENPP1. Remarkably, Enpp1H362A mice were resistant to HSV-1 infection, demonstrating the antiviral role of endogenous extracellular cGAMP. The ENPP1H362A mutation is the first genetic tool to enable exploration of extracellular cGAMP biology in a wide range of tissues and diseases.
The conserved zinc-finger protein GTSF1 helps PIWI proteins achieve their full catalytic potential
Authors: Arif Amena , Bailey Shannon , Izumi Natsuko , Anzelon Todd A. , Ozata Deniz M. , Andersson Cecilia , Gainetdinov Ildar , MacRae Ian J. , Tomari Yukihide , Zamore Phillip D. 
Published: May 2021

AbstractArgonaute proteins use nucleic acid guides to find and bind specific DNA or RNA target sequences. Argonaute proteins can be found in all kingdoms of life, and play diverse biological functions including genome defense, gene regulation, and chromosome partitioning. Many Argonautes retain their ancestral endoribonuclease activity, cleaving the phosphodiester bond between target nucleotides t10 and t11. In animals, a specialized class of Argonautes, the PIWI proteins, use 21–35 nt PIWI-interacting RNAs (piRNAs) to direct transposon silencing, protect the germline genome, and regulate gene expression during gametogenesis1. The piRNA pathway is required for fertility in one or both sexes of nearly all animals. Both piRNA production and function require RNA cleavage catalyzed by PIWI proteins. Spermatogenesis in mice and other placental mammals requires three distinct, developmentally regulated PIWI proteins: MIWI (PIWIL1), MILI (PIWIL2), and MIWI2 (PIWIL4)2–4. The piRNA-guided endoribonuclease activities of MIWI and MILI are essential to produce functional sperm5, 6. piRNA-directed silencing in mice and insects also requires Gametocyte-Specific Factor 1 (GTSF1), a PIWI-associated protein of unknown function7–12. Here, we report that GTSF1 potentiates the weak, intrinsic, piRNA-directed RNA cleavage activities of PIWI proteins, transforming them into efficient endoribonucleases. GTSF1 represents the first example of an auxiliary protein that potentiates the catalytic activity of an Argonaute protein.
Fertility costs of cryptic viral infections in a model social insect
Authors: Chapman Abigail , Amiri Esmaeil , Han Bin , McDermott Erin , Rueppell Olav , Tarpy David R , Foster Leonard J , McAfee Alison 
Published: May 2021

AbstractDeclining insect populations emphasize the importance of understanding the drivers underlying reductions in insect fitness. Here, we investigated viruses as a threat to social insect reproduction, using honey bees as a model species. We report that in a sample of N = 93 honey bee (Apis mellifera) queens from nine beekeeping operations across a wide geographic range, high levels of natural viral infection are associated with decreased ovary mass. We confirmed this finding in an independent sample of N = 54 queens. Failed (poor quality) queens displayed higher levels of viral infection, reduced sperm viability, smaller ovaries, and altered ovary protein composition compared to healthy queens. We experimentally infected queens with Israeli acute paralysis virus (IAPV) and found that the ovary masses of IAPV-injected queens were significantly smaller than control queens, demonstrating a causal relationship between viral infection and ovary size. Queens injected with IAPV also had significantly lower expression of vitellogenin, the main source of nutrition deposited into developing oocytes, and higher levels of heat-shock proteins (HSPs), which are part of the honey bee’s antiviral response. This work together shows that viral infections occurring naturally in the field are compromising queen reproductive success.