bluuebunny/crossref_metadata_2025_split huggingface dataset:
A two-hit epistasis model prevents core genome disharmony in recombining bacteria
Authors: Taylor Aidan J. , Yahara Koji , Pascoe Ben , Mageiros Leonardos , Mourkas Evangelos , Calland Jessica K , Puranen Santeri , Hitchings Matthew D. , Jolley Keith A. , Kobras Carolin M. , Bayliss Sion , Williams Nicola J. , van Vliet Arnoud H. M. , Parkhill Julian , Maiden Martin C. J. , Corander Jukka , Hurst Laurence D , Falush Daniel , Keim Paul , Didelot Xavier , Kelly David J. , Sheppard Samuel K. 
Published: March 2021

Significance StatementGenetic exchange among bacteria shapes the microbial world. From the acquisition of antimicrobial resistance genes to fundamental questions about the nature of bacterial species, this powerful evolutionary force has preoccupied scientists for decades. However, the mixing of genes between species rests on a paradox. On one hand, promoting adaptation by conferring novel functionality, on the other potentially introducing disharmonious gene combinations (negative epistasis) that will be selected against. Taking an interdisciplinary approach to analyse natural populations of the enteric bacteriaCampylobacter, an ideal example of long-range admixture, we demonstrate that genes can independently transfer across species boundaries and rejoin in epistasis in a recipient genome. This challenges conventional ideas and highlights the possibility of single step evolution by saltation.AbstractRecombination of short DNA fragments via horizontal gene transfer (HGT) can both introduce beneficial alleles and create genomic disharmony through negative epistasis. For non-core (accessory) genes, the negative epistatic cost is likely to be minimal because the incoming genes have not co-evolved with the recipient genome. By contrast, for the core genome, interspecific recombination is expected to be rare because disruptive allelic replacement is likely to introduce negative epistasis. Why then is homologous recombination common in the core of bacterial genomes? To understand this enigma we take advantage of an exceptional model system, the common enteric pathogensCampylobacter jejuniandCampylobacter coli, that are known for very high magnitude interspecies gene flow in the core genome. As expected, HGT does indeed disrupt co-adapted allele pairings (negative epistasis). However, multiple HGT events enable recovery of the genome’s co-adaption between introgressing alleles, even in core metabolism genes (e.g., formate dehydrogenase). These findings demonstrate that, even for complex traits, genetic coalitions can be decoupled, transferred and independently reinstated in a new genetic background – facilitating transition between fitness peaks. In this example, the two-step recombinational process is associated withC. colithat are adapted to the agricultural niche.
First isolation of virulentTenacibaculum maritimumstrains from diseased orbicular batfish (Platax orbicularis) farmed in Tahiti Island
Authors: Lopez Pierre , Saulnier Denis , Swarup-Gaucher Shital , David Rarahu , Lau Christophe , Taputuarai Revahere , Belliard Corinne , Basset Caline , Labrune Victor , Marie Arnaud , Bernardet Jean François , Duchaud Eric 
Published: March 2021

AbstractThe orbicular batfish (Platax orbicularis), also called ‘Paraha peue’ in Tahitian, is the most important marine fish species reared in French Polynesia. Sudden and widespread outbreaks of severe ‘white-patch disease’ have occurred since 2011 in batfish farms one to three weeks after the transfer of juveniles from bio-secured hatcheries to lagoon cages. With cumulative mortality ranging from 20 to 90%, the sustainability of aquaculture of this species is severely threatened.In this study, we describe for the first time the isolation from diseased batfish of several strains belonging to the speciesTenacibaculum maritimum, a major pathogen of many marine fish species. Histopathological analysis, an experimental bath challenge and a field monitoring study showed thatT. maritimumis associated with white-patch disease. Moreover, molecular and serological analyses performed on representative strains revealed some degree of genetic diversity among the isolates, a finding of primary importance for epidemiological studies and for the development of management and control strategies such as vaccination.
Infective prey leads to a partial role reversal in a predator-prey interaction
Authors: Kaitala Veijo , Koivu-Jolma Mikko , Laakso Jouni 
Published: March 2021

AbstractAn infective prey has the potential to infect, kill and consume its predator. Such a prey-predator relationship fundamentally differs from the classical Lotka-Volterra predator-prey premise because the prey can directly profit from the predator as a growth resource. Here we present a population dynamics model of partial role reversal in the predator-prey interaction. We parametrize the model to represent the predator-prey interaction of sea cucumberApostichopus japonicusand bacteriumVibrio splendidus. We observe that two major factors stabilize the predator-prey interaction. First, the partial role reversal in the predator-prey community stabilizes the predator-prey interaction. Second, if the predator is a generalist and follows the type I functional response in attacking the prey, the predator-prey interaction is stable. We also analysed the conditions for species extinction. The extinction of the prey,V. splendidus, may occur when its growth rate is low, or in the absence of infectivity. The extinction of the predator,A. japonicus, may follow if either the infectivity of the prey is high or a moderately infective prey is abundant. We conclude that partial role reversal is an underestimated subject in predator-prey studies.
Amplitude and phase coupling optimize information transfer between brain networks that function at criticality
Authors: Avramiea Arthur-Ervin , Masood Anas , Mansvelder Huibert D. , Linkenkaer-Hansen Klaus 
Published: March 2021

AbstractBrain function depends on segregation and integration of information processing in brain networks often separated by long-range anatomical connections. Neuronal oscillations orchestrate such distributed processing through transient amplitude and phase coupling, yet surprisingly little is known about local network properties facilitating these functional connections. Here, we test whether criticality—a dynamical state characterized by scale-free oscillations—optimizes the capacity of neuronal networks to couple through amplitude or phase, and transfer information. We coupledin siliconetworks with varying excitatory and inhibitory connectivity, and found that phase coupling emerges at criticality, and that amplitude coupling, as well as information transfer, are maximal when networks are critical. Importantly, regulating criticality through neuromodulation of synaptic strength showed that critical dynamics—as opposed to a static ratio of excitatory and inhibitory connections—optimize network coupling and information transfer. Our data support the idea that criticality is important for local and global information processing and may help explain why brain disorders characterized by local alterations in criticality also exhibit impaired long-range synchrony, even prior to degeneration of axonal connections.
A Bioinformatic and Empiric Exploration of Prokaryotic Argonautes as Novel Programmable Endonuclease Systems
Authors: Salic Sejla , Sieber Anna , Barbaria Samir , Vasilyev Anatoly , Papadimou Elisavet , Milosavljevic Nevena , Klapholz Benjamin , Sivapalan Rohan , Collingwood Trevor , Henley Tom , Choudhry Modassir , Bürckstümmer Tilmann 
Published: March 2021

ABSTRACTArgonautes are nucleases that can be programmed by short oligonucleotides to cleave complementary sequences. Here, we performed an unbiased bioinformatic search to mine bacterial genomes for prokaryotic Argonautes (pAgos) harboring a PIWI domain. Our search identified 3,033 pAgos in total, of which 1,464 portend to the subgroup of long pAgos with more than 600 amino acids. We purified a subset of 49 pAgos which were found in proximity to helicases and tested their nuclease activityin vitro. Ten of these were active towards single-stranded DNA substrates and this activity could be programmed by exogenous guide DNAs or RNAs. Cleavage of double-stranded plasmid DNA was much less readily observed and was fostered by elevated temperatures or exogenous addition of a DNA single-strand binding protein (ET-SSB). The efficiency of pAgo-mediated plasmid cleavage was dependent on the DNA target sequence as well as the surrounding sequence, suggesting that unwinding of the DNA double helix was a limiting factor. Intriguingly, we identified a cluster of pAgos from the Clostridial clade which was active at 37°C and activity was enhanced by exogenous ET-SSB. This suggests that Clostridial pAgos may be particularly suited to catalyze DNA double-strand cleavage and implies that such pAgos may be repurposed as gene editing tools in future.
Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations
Authors: Conrad Roth E. , Viver Tomeu , Gago Juan F. , Hatt Janet K. , Venter Fanus , Rosselló-Móra Ramon , Konstantinidis Konstantinos T. 
Published: March 2021

AbstractMetagenomic surveys have revealed that natural microbial communities are predominantly composed of sequence-discrete, species-like populations but the genetic and/or ecological mechanisms that maintain such populations remain speculative, limiting our understanding of population speciation and adaptation to environmental perturbations. To address this knowledge gap, we sequenced 112Salinibacter ruberisolates and 12 companion metagenomes recovered from four adjacent saltern ponds in Mallorca, Spain that were experimentally manipulated to dramatically alter salinity and light intensity, the two major drivers of these ecosystems. Our analyses showed that the pangenome of the localSal. ruberpopulation is open and similar in size (∼15,000 genes) to that of randomly sampledEscherichia coligenomes. While most of the accessory (non-core) genes showed lowin situcoverage based on the metagenomes compared to the core genes, indicating that they were functionally unimportant and/or ephemeral, 3.49% of them became abundant when salinity (but not light intensity) conditions changed and encoded for functions related to osmoregulation. Nonetheless, the ecological advantage of these genes, while significant, was apparently not strong enough to purge diversity within the population. Collectively, our results revealed a possible mechanism for how this immense gene diversity is maintained, which has implications for the prokaryotic species concept.Significance StatementThe pangenomes of bacterial species, i.e., the number of non-redundant genes carried by members of the species, can be enormous based on the genome sequencing of isolates from various sites around the globe and different years. However, to what extent this pattern of gene diversity applies to natural bacterial populations, i.e., strains co-occurring in the same site, and the value of this diversity for population adaptation during environmental transition remains unclear. This study showed that while the pangenome of a natural population can be similarly large, only a small fraction of the pangenome appears to be functionally important when conditions change. Taken together, these results provided quantitative insights into the extent and functional significance of the accessory pangenome of a natural, species-like population.
A single amino acid polymorphism in a conserved effector of the multihost blast fungus pathogen expands host-target binding spectrum
Authors: Bentham Adam R. , Petit-Houdenot Yohann , Win Joe , Chuma Izumi , Terauchi Ryohei , Banfield Mark J. , Kamoun Sophien , Langner Thorsten 
Published: March 2021

AbstractAccelerated gene evolution is a hallmark of pathogen adaptation and specialization following host-jumps. However, the molecular processes associated with adaptive evolution between host-specific lineages of a multihost plant pathogen remain poorly understood. In the blast fungusMagnaporthe oryzae(Syn.Pyricularia oryzae),host specialization on different grass hosts is generally associated with dynamic patterns of gain and loss of virulence effector genes that tend to define the distinct genetic lineages of this pathogen. Here, we unravelled the biochemical and structural basis of adaptive evolution of APikL2, an exceptionally conserved paralog of the well-studied rice-lineage specific effector AVR-Pik. Whereas AVR-Pik and other members of the six-gene AVR-Pik family show specific patterns of presence/absence polymorphisms between grassspecific lineages ofM. oryzae,APikL2 stands out by being ubiquitously present in all blast fungus lineages from 13 different host species. Using biochemical, biophysical and structural biology methods, we show that a single aspartate to asparagine polymorphism expands the binding spectrum of APikL2 to host proteins of the heavy-metal associated (HMA) domain family. This mutation maps to one of the APikL2-HMA binding interfaces and contributes to an altered hydrogen-bonding network. By combining phylogenetic ancestral reconstruction with an analysis of the structural consequences of allelic diversification, we revealed a common mechanism of effector specialization in the AVR-Pik/APikL2 family that involves two major HMA-binding interfaces. Together, our findings provide a detailed molecular evolution and structural biology framework for diversification and adaptation of a fungal pathogen effector family following host-jumps.
Analysis of the PcrA-RNA polymerase complex reveals a helicase interaction motif and a role for PcrA/UvrD helicase in the suppression of R-loops
Authors: Urrutia-Irazabal I. , Ault  , Sobott F. , Savery N.J. , Dillingham M.S. 
Published: March 2021

AbstractThe PcrA/UvrD helicase binds directly to RNA polymerase (RNAP) but the structural basis for this interaction and its functional significance have remained unclear. In this work we used biochemical assays and hydrogen-deuterium exchange coupled to mass spectrometry to study the PcrA-RNAP complex. We find that PcrA binds tightly to a transcription elongation complex in a manner dependent on protein:protein interaction with the conserved PcrA C-terminal Tudor domain. The helicase binds predominantly to two positions on the surface of RNAP. The PcrA C-terminal domain engages a conserved region in a lineage-specific insert within the β subunit which we identify as a helicase interaction motif present in many other PcrA partner proteins, including the nucleotide excision repair factor UvrB. The catalytic core of the helicase binds near the RNA and DNA exit channels and blocking PcrA activityin vivoleads to the accumulation of R-loops. We propose a role for PcrA as an R-loop suppression factor that helps to minimise conflicts between transcription and other processes on DNA including replication.
DNA methylation clocks show slower progression of aging in naked mole-rat queens
Authors: Horvath Steve , Haghani Amin , Macoretta Nicholas , Ablaeva Julia , Zoller Joseph A. , Li Caesar Z. , Zhang Joshua , Takasugi Masaki , Zhao Yang , Rydkina Elena , Zhang Zhihui , Emmrich Stephan , Raj Ken , Seluanov Andrei , Faulkes Chris G. , Gorbunova Vera 
Published: March 2021

ABSTRACTNaked mole-rats (NMRs) live an exceptionally long life, appear not to exhibit age-related decline in physiological capacity, and are seemingly resistant to age-related diseases. However, it has been unknown whether NMRs also evade aging according to a primary hallmark of aging: epigenetic changes. To address this question, we generated DNA methylation profiles from 329 tissues from animals of known age, at loci that are highly conserved between mammalian species, using a custom Infinium array (HorvathMammalMethylChip40). We observed strong aging effects on NMR DNA methylation, from which we developed seven highly accurate age estimators (epigenetic clocks) for several tissues (pan-tissue, blood, kidney clock, liver clock, skin clock) and two dual species (human-NMR) clocks. By identifying age-related cytosine methylation that are shared between NMR and humans, but not with the mouse, we identified genes and cellular pathways that impinge on developmental and metabolic processes that are potentially involved in NMR and human longevity. The NMR epigenetic clocks revealed that breeding NMR queens age more slowly than non-breeders, a feature that is also observed in some eusocial insects. CpGs associated with queen status were located near developmental genes and those that are regulated by theLHX3transcription factor that controls pituitary development. In summary, our study demonstrates that despite a phenotype of reduced senescence, the NMR ages epigenetically through developmental and metabolic processes, and that NMR queens age more slowly than non-breeders.
A ROR2 coding variant is associated with craniofacial variation in domestic pigeons
Authors: Boer Elena F. , Van Hollebeke Hannah F. , Holt Carson , Yandell Mark , Shapiro Michael D. 
Published: March 2021

SummaryVertebrate craniofacial morphogenesis is a highly orchestrated process that is directed by evolutionarily conserved developmental pathways 1,2. Within species, canalized developmental programs typically produce only modest morphological variation. However, as a result of millennia of artificial selection, the domestic pigeon (Columba livia) displays radical variation in craniofacial morphology within a single species. One of the most striking cases of pigeon craniofacial variation is the short beak phenotype, which has been selected in numerous breeds. Classical genetic experiments suggest that pigeon beak length is regulated by a small number of genetic factors, one of which is sex-linked (Ku2 locus) 3–5. However, the molecular genetic underpinnings of pigeon craniofacial variation remain unknown. To determine the genetic basis of the short beak phenotype, we used geometric morphometrics and quantitative trait loci (QTL) mapping on an F2 intercross between a short-beaked Old German Owl (OGO) and a medium-beaked Racing Homer (RH). We identified a single locus on the Z-chromosome that explains a majority of the variation in beak morphology in the RH x OGO F2 population. In complementary comparative genomic analyses, we found that the same locus is also strongly differentiated between breeds with short and medium beaks. Within the differentiated Ku2 locus, we identified an amino acid substitution in the non-canonical Wnt receptor ROR2 as a putative regulator of pigeon beak length. The non-canonical Wnt (planar cell polarity) pathway serves critical roles in vertebrate neural crest cell migration and craniofacial morphogenesis 6,7. In humans, homozygous ROR2 mutations cause autosomal recessive Robinow syndrome, a rare congenital disorder characterized by skeletal abnormalities, including a widened and shortened facial skeleton 8,9. Our results illustrate how the extraordinary craniofacial variation among pigeons can reveal genetic regulators of vertebrate craniofacial diversity.
Implications of cholesterol and sphingomyelin in STING phosphorylation by TBK1
Authors: Takahashi Kanoko , Niki Takahiro , Ogawa Emari , Fumika Kiku , Nishioka Yu , Sawa Masaaki , Arai Hiroyuki , Mukai Kojiro , Taguchi Tomohiko 
Published: March 2021

AbstractStimulator of interferon genes (STING) is essential for the type I interferon response induced by microbial DNA from virus or self-DNA from mitochondria/nuclei. In response to emergence of such DNAs in the cytosol, STING translocates from the endoplasmic reticulum (ER) to the Golgi, and activates TANK-binding kinase 1 (TBK1) at the trans-Golgi network (TGN). Activated TBK1 then phosphorylates STING at Ser365, generating an interferon regulatory factor 3 (IRF3)-docking site on STING. How this reaction proceeds specifically at the TGN remains poorly understood. Here we report a cell-free reaction in which endogenous STING is phosphorylated by TBK1. The reaction utilizes microsomal membrane fraction prepared from TBK1-knockout (KO) cells and recombinant TBK1. We observed agonist-, TBK1-, “ER-to-Golgi” traffic-, and palmitoylation-dependent phosphorylation of STING at Ser365, mirroring the nature of STING phosphorylationin vivo.Treating the microsomal membrane fraction with sphingomyelinase or methyl-β-cyclodextrin, an agent to extract cholesterol from membranes, suppressed the phosphorylation of STING by TBK1. Given the enrichment of sphingomyelin and cholesterol in the TGN, these results may provide the molecular basis underlying the specific phosphorylation reaction of STING at the TGN.
The impact of a humanitarian disaster on the working approach of accountants: a study of contingent effects
Authors: Carungu Jonida , Di Pietra Roberto , Molinari Matteo 
Published: March 2021

PurposeThe purpose of this paper is to investigate how a humanitarian disaster as coronavirus disease 2019 (COVID-19) shapes the working approach of accountants. This research is motivated by the call for more in-depth analyses of how COVID-19 affects the work, role and human condition of accountants. The study aims to discover the contingent effects, based on the contingency theory, on accountants' work due to a disaster like COVID-19.Design/methodology/approachThis is a qualitative study with an action research approach. The research relies on semi-structured interviews and the active participation of a co-author in a professional organisation under investigation. Data collected are analysed using thematic analysis through an inductive interpretative approach.FindingsThe contingent shock embodies both a reactive and adaptive approach in the accountants' professional work. From a theoretical perspective, this study identifies nine contingent phases related to shock. The accountants' experience helps to understand how the COVID-19 pandemic contingently shapes the working approach of accountants with both short- and long-term organisational implications.Originality/valueBased on the literature survey, this is the first study to adopt an action research approach to engage with the complex dynamics involved in the social context of COVID-19 by discovering the effective actions, reactions, changes and solutions to problems experienced by professional accountants. This approach helps to build knowledge that enhances professional, and community practises by answering the call for multidisciplinary contributions in accounting to address the global COVID-19 crisis, its impacts and opportunities for future research.