bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allelic polymorphism shapes community function in evolving Pseudomonas aeruginosa populations
Authors: Azimi Sheyda , Roberts Aled E L , Peng Shengyun , Weitz Joshua S , McNally Alan , Brown Samuel P , Diggle Stephen P 
Published: April 2020

Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that chronically infects the lungs of individuals with cystic fibrosis (CF) by forming antibiotic-resistant biofilms. Emergence of phenotypically diverse isolates within CF P. aeruginosa populations has previously been reported; however, the impact of heterogeneity on social behaviors and community function is poorly understood. Here we describe how this heterogeneity impacts on behavioral traits by evolving the strain PAO1 in biofilms grown in a synthetic sputum medium for 50 days. We measured social trait production and antibiotic tolerance, and used a metagenomic approach to analyze and assess genomic changes over the duration of the evolution experiment. We found that (i) evolutionary trajectories were reproducible in independently evolving populations; (ii) over 60% of genomic diversity occurred within the first 10 days of selection. We then focused on quorum sensing (QS), a well-studied P. aeruginosa trait that is commonly mutated in strains isolated from CF lungs. We found that at the population level, (i) evolution in sputum medium selected for decreased the production of QS and QS-dependent traits; (ii) there was a significant correlation between lasR mutant frequency, the loss of protease, and the 3O-C12-HSL signal, and an increase in resistance to clinically relevant β-lactam antibiotics, despite no previous antibiotic exposure. Overall, our findings provide insights into the effect of allelic polymorphism on community functions in diverse P. aeruginosa populations. Further, we demonstrate that P. aeruginosa population and evolutionary dynamics can impact on traits important for virulence and can lead to increased tolerance to β-lactam antibiotics.
Dark septate endophyte improves salt tolerance of native and invasive lineages of Phragmites australis
Authors: Gonzalez Mateu Martina , Baldwin Andrew H , Maul Jude E , Yarwood Stephanie A 
Published: April 2020

Abstract
Fungal endophytes can improve plant tolerance to abiotic stress. However, the role of these plant–fungal interactions in invasive species ecology and their management implications remain unclear. This study characterized the fungal endophyte communities of native and invasive lineages of Phragmites australis and assessed the role of dark septate endophytes (DSE) in salt tolerance of this species. We used Illumina sequencing to characterize root fungal endophytes of contiguous stands of native and invasive P. australis along a salinity gradient. DSE colonization was assessed throughout the growing season in the field, and effects of fungal inoculation on salinity tolerance were investigated using laboratory and greenhouse studies. Native and invasive lineages had distinct fungal endophyte communities that shifted across the salinity gradient. DSE colonization was greater in the invasive lineage and increased with salinity. Laboratory studies showed that DSE inoculation increased P. australis seedling survival under salt stress; and a greenhouse assay revealed that the invasive lineage had higher aboveground biomass under mesohaline conditions when inoculated with a DSE. We observed that P. australis can establish mutualistic associations with DSE when subjected to salt stress. This type of plant–fungal association merits further investigation in integrated management strategies of invasive species and restoration of native Phragmites.
Shared genetic etiology between obsessive-compulsive disorder, obsessive-compulsive symptoms in the population, and insulin signaling
Authors: Bralten Janita , Widomska Joanna , Witte Ward De , Yu Dongmei , Mathews Carol A. , Scharf Jeremiah M. , Buitelaar Jan , Crosbie Jennifer , Schachar Russell , Arnold Paul , Lemire Mathieu , Burton Christie L. , Franke Barbara , Poelmans Geert 
Published: April 2020

AbstractObsessive-compulsive symptoms (OCS) in the population have been linked to obsessive-compulsive disorder (OCD) in genetic and epidemiological studies. Insulin signaling has been implicated in OCD. We extend previous work by assessing genetic overlap between OCD, population-based OCS, and central nervous system (CNS) and peripheral insulin signaling. We conducted genome-wide association studies (GWASs) in the population-based Philadelphia Neurodevelopmental Cohort (PNC, 650 children and adolescents) of the total OCS score and six OCS factors from an exploratory factor analysis of 22 questions. Subsequently, we performed polygenic risk score (PRS)-based analysis to assess shared genetic etiologies between clinical OCD (using GWAS data from the Psychiatric Genomics Consortium), the total OCS score and OCS factors. We then performed gene-set analyses with a set of OCD-linked genes centered around CNS insulin-regulated synaptic function and PRS-based analyses for five peripheral insulin signaling-related traits. For validation purposes, we explored data from the independent Spit for Science population cohort (5,047 children and adolescents). In the PNC, we found a significant shared genetic etiology between OCD and ‘guilty taboo thoughts’. In the Spit for Science cohort, we additionally observed genetic sharing between ‘symmetry/counting/ordering’ and ‘contamination/cleaning’. The CNS insulin-linked gene-set also associated with ‘symmetry/counting/ordering’ in the PNC. Further, we identified genetic sharing between peripheral insulin signaling-related traits: type 2 diabetes with ‘aggressive taboo thoughts’, and levels of fasting insulin and 2 h glucose with OCD. In conclusion, OCD, OCS in the population and insulin-related traits share genetic risk factors, indicating a common etiological mechanism underlying somatic and psychiatric disorders.
The nuclear envelope: target and mediator of the apoptotic process
Authors: Lindenboim Liora , Zohar Hila , Worman Howard J. , Stein Reuven 
Published: April 2020

AbstractApoptosis is characterized by the destruction of essential cell organelles, including the cell nucleus. The nuclear envelope (NE) separates the nuclear interior from the cytosol. During apoptosis, the apoptotic machinery, in particular caspases, increases NE permeability by cleaving its proteins, such as those of the nuclear pore complex (NPC) and the nuclear lamina. This in turns leads to passive diffusion of cytosolic apoptogenic proteins, such as caspases and nucleases, through NPCs into the nucleus and the subsequent breakdown of the NE and destruction of the nucleus. However, NE leakiness at early stages of the apoptotic process can also occur in a caspase-independent manner, where Bax, by a non-canonical action, promotes transient and repetitive localized generation and subsequent rupture of nuclear protein-filled nuclear bubbles. This NE rupture leads to discharge of apoptogenic nuclear proteins from the nucleus to the cytosol, a process that can contribute to the death process. Therefore, the NE may play a role as mediator of cell death at early stages of apoptosis. The NE can also serve as a platform for assembly of complexes that regulate the death process. Thus, the NE should be viewed as both a mediator of the cell death process and a target.
Phosphorylation of cGAS by CDK1 impairs self-DNA sensing in mitosis
Authors: Zhong Li , Hu Ming-Ming , Bian Li-Jun , Liu Ying , Chen Qiang , Shu Hong-Bing 
Published: April 2020

AbstractThe cyclic GMP-AMP synthase (cGAS) is a widely used DNA sensor, which detects cytosolic DNA species without a preference of self or non-self microbial DNA in interphase to initiate innate immune response. How cGAS is regulated to avoid self-DNA sensing upon nuclear envelope breakdown (NEBD) during mitosis remains enigmatic. Here we show that cGAS is mostly localized in the cytoplasm in interphase and rapidly translocated to chromosomes upon NEBD in mitosis. The major mitotic kinase CDK1-cyclin B complex phosphorylates human cGAS at S305 or mouse cGAS at S291, which inhibits its ability to synthesize cGAMP upon mitotic entry. The type 1 phosphatase PP1 dephosphorylates cGAS upon mitotic exit to enable its DNA sensing ability. Our findings reveal a mechanism on how the DNA sensor cGAS is post-translationally regulated by cell cycle-dependent enzymes to ensure its proper activation for host defense of cytosolic DNA in interphase and inert to self-DNA in mitosis.
Repurposing a chemosensory macromolecular machine
Authors: Ortega Davi R. , Yang Wen , Subramanian Poorna , Mann Petra , Kjær Andreas , Chen Songye , Watts Kylie J. , Pirbadian Sahand , Collins David A. , Kooger Romain , Kalyuzhnaya Marina G. , Ringgaard Simon , Briegel Ariane , Jensen Grant J. 
Published: April 2020

AbstractHow complex, multi-component macromolecular machines evolved remains poorly understood. Here we reveal the evolutionary origins of the chemosensory machinery that controls flagellar motility in Escherichia coli. We first identify ancestral forms still present in Vibrio cholerae, Pseudomonas aeruginosa, Shewanella oneidensis and Methylomicrobium alcaliphilum, characterizing their structures by electron cryotomography and finding evidence that they function in a stress response pathway. Using bioinformatics, we trace the evolution of the system through γ-Proteobacteria, pinpointing key evolutionary events that led to the machine now seen in E. coli. Our results suggest that two ancient chemosensory systems with different inputs and outputs (F6 and F7) existed contemporaneously, with one (F7) ultimately taking over the inputs and outputs of the other (F6), which was subsequently lost.
Observation of giant spin-split Fermi-arc with maximal Chern number in the chiral topological semimetal PtGa
Authors: Yao Mengyu , Manna Kaustuv , Yang Qun , Fedorov Alexander , Voroshnin Vladimir , Valentin Schwarze B. , Hornung Jacob , Chattopadhyay S. , Sun Zhe , Guin Satya N. , Wosnitza Jochen , Borrmann Horst , Shekhar Chandra , Kumar Nitesh , Fink Jörg , Sun Yan , Felser Claudia 
Published: April 2020

AbstractNon-symmorphic chiral topological crystals host exotic multifold fermions, and their associated Fermi arcs helically wrap around and expand throughout the Brillouin zone between the high-symmetry center and surface-corner momenta. However, Fermi-arc splitting and realization of the theoretically proposed maximal Chern number rely heavily on the spin-orbit coupling (SOC) strength. In the present work, we investigate the topological states of a new chiral crystal, PtGa, which has the strongest SOC among all chiral crystals reported to date. With a comprehensive investigation using high-resolution angle-resolved photoemission spectroscopy, quantum-oscillation measurements, and state-of-the-art ab initio calculations, we report a giant SOC-induced splitting of both Fermi arcs and bulk states. Consequently, this study experimentally confirms the realization of a maximal Chern number equal to ±4 in multifold fermionic systems, thereby providing a platform to observe large-quantized photogalvanic currents in optical experiments.
Enabling room temperature ferromagnetism in monolayer MoS2 via in situ iron-doping
Authors: Fu Shichen , Kang Kyungnam , Shayan Kamran , Yoshimura Anthony , Dadras Siamak , Wang Xiaotian , Zhang Lihua , Chen Siwei , Liu Na , Jindal Apoorv , Li Xiangzhi , Pasupathy Abhay N. , Vamivakas A. Nick , Meunier Vincent , Strauf Stefan , Yang Eui-Hyeok 
Published: April 2020

AbstractTwo-dimensional semiconductors, including transition metal dichalcogenides, are of interest in electronics and photonics but remain nonmagnetic in their intrinsic form. Previous efforts to form two-dimensional dilute magnetic semiconductors utilized extrinsic doping techniques or bulk crystal growth, detrimentally affecting uniformity, scalability, or Curie temperature. Here, we demonstrate an in situ substitutional doping of Fe atoms into MoS2 monolayers in the chemical vapor deposition growth. The iron atoms substitute molybdenum sites in MoS2 crystals, as confirmed by transmission electron microscopy and Raman signatures. We uncover an Fe-related spectral transition of Fe:MoS2 monolayers that appears at 2.28 eV above the pristine bandgap and displays pronounced ferromagnetic hysteresis. The microscopic origin is further corroborated by density functional theory calculations of dipole-allowed transitions in Fe:MoS2. Using spatially integrating magnetization measurements and spatially resolving nitrogen-vacancy center magnetometry, we show that Fe:MoS2 monolayers remain magnetized even at ambient conditions, manifesting ferromagnetism at room temperature.
Exciton diffusion in two-dimensional metal-halide perovskites
Authors: Seitz Michael , Magdaleno Alvaro J. , Alcázar-Cano Nerea , Meléndez Marc , Lubbers Tim J. , Walraven Sanne W. , Pakdel Sahar , Prada Elsa , Delgado-Buscalioni Rafael , Prins Ferry 
Published: April 2020

AbstractTwo-dimensional layered perovskites are attracting increasing attention as more robust analogues to the conventional three-dimensional metal-halide perovskites for both light harvesting and light emitting applications. However, the impact of the reduced dimensionality on the optoelectronic properties remains unclear, particularly regarding the spatial dynamics of the excitonic excited state within the two-dimensional plane. Here, we present direct measurements of exciton transport in single-crystalline layered perovskites. Using transient photoluminescence microscopy, we show that excitons undergo an initial fast diffusion through the crystalline plane, followed by a slower subdiffusive regime as excitons get trapped. Interestingly, the early intrinsic diffusivity depends sensitively on the choice of organic spacer. A clear correlation between lattice stiffness and diffusivity is found, suggesting exciton–phonon interactions to be dominant in the spatial dynamics of the excitons in perovskites, consistent with the formation of exciton–polarons. Our findings provide a clear design strategy to optimize exciton transport in these systems.
Latitudinal gradient in dairy production with the introduction of farming in Atlantic Europe
Authors: Cubas Miriam , Lucquin Alexandre , Robson Harry K. , Colonese André Carlo , Arias Pablo , Aubry Bruno , Billard Cyrille , Jan Denis , Diniz Mariana , Fernandes Ricardo , Fábregas Valcarce Ramón , Germain-Vallée Cécile , Juhel Laurent , de Lombera-Hermida Arturo , Marcigny Cyril , Mazet Sylvain , Marchand Grégor , Neves César , Ontañón-Peredo Roberto , Rodríguez-Álvarez Xose Pedro , Simões Teresa , Zilhão João , Craig Oliver E. 
Published: April 2020

AbstractThe introduction of farming had far-reaching impacts on health, social structure and demography. Although the spread of domesticated plants and animals has been extensively tracked, it is unclear how these nascent economies developed within different environmental and cultural settings. Using molecular and isotopic analysis of lipids from pottery, here we investigate the foods prepared by the earliest farming communities of the European Atlantic seaboard. Surprisingly, we find an absence of aquatic foods, including in ceramics from coastal sites, except in the Western Baltic where this tradition continued from indigenous ceramic using hunter-gatherer-fishers. The frequency of dairy products in pottery increased as farming was progressively introduced along a northerly latitudinal gradient. This finding implies that early farming communities needed time to adapt their economic practices before expanding into more northerly areas. Latitudinal differences in the scale of dairy production might also have influenced the evolution of adult lactase persistence across Europe.
Integrative functional genomics decodes herpes simplex virus 1
Authors: Whisnant Adam W. , Jürges Christopher S. , Hennig Thomas , Wyler Emanuel , Prusty Bhupesh , Rutkowski Andrzej J. , L’hernault Anne , Djakovic Lara , Göbel Margarete , Döring Kristina , Menegatti Jennifer , Antrobus Robin , Matheson Nicholas J. , Künzig Florian W. H. , Mastrobuoni Guido , Bielow Chris , Kempa Stefan , Liang Chunguang , Dandekar Thomas , Zimmer Ralf , Landthaler Markus , Grässer Friedrich , Lehner Paul J. , Friedel Caroline C. , Erhard Florian , Dölken Lars 
Published: April 2020

AbstractThe predicted 80 open reading frames (ORFs) of herpes simplex virus 1 (HSV-1) have been intensively studied for decades. Here, we unravel the complete viral transcriptome and translatome during lytic infection with base-pair resolution by computational integration of multi-omics data. We identify a total of 201 transcripts and 284 ORFs including all known and 46 novel large ORFs. This includes a so far unknown ORF in the locus deleted in the FDA-approved oncolytic virus Imlygic. Multiple transcript isoforms expressed from individual gene loci explain translation of the vast majority of ORFs as well as N-terminal extensions (NTEs) and truncations. We show that NTEs with non-canonical start codons govern the subcellular protein localization and packaging of key viral regulators and structural proteins. We extend the current nomenclature to include all viral gene products and provide a genome browser that visualizes all the obtained data from whole genome to single-nucleotide resolution.
The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks
Authors:   International Committee on Taxonomy of Viruses Executive Committee, Gorbalenya Alexander E. , Krupovic Mart , Mushegian Arcady , Kropinski Andrew M. , Siddell Stuart G. , Varsani Arvind , Adams Michael J. , Davison Andrew J. , Dutilh Bas E. , Harrach Balázs , Harrison Robert L. , Junglen Sandra , King Andrew M. Q. , Knowles Nick J. , Lefkowitz Elliot J. , Nibert Max L. , Rubino Luisa , Sabanadzovic Sead , Sanfaçon Hélène , Simmonds Peter , Walker Peter J. , Zerbini F. Murilo , Kuhn Jens H. 
Published: April 2020

AbstractVirus taxonomy emerged as a discipline in the middle of the twentieth century. Traditionally, classification by virus taxonomists has been focussed on the grouping of relatively closely related viruses. However, during the past few years, the International Committee on Taxonomy of Viruses (ICTV) has recognized that the taxonomy it develops can be usefully extended to include the basal evolutionary relationships among distantly related viruses. Consequently, the ICTV has changed its Code to allow a 15-rank classification hierarchy that closely aligns with the Linnaean taxonomic system and may accommodate the entire spectrum of genetic divergence in the virosphere. The current taxonomies of three human pathogens, Ebola virus, severe acute respiratory syndrome coronavirus and herpes simplex virus 1 are used to illustrate the impact of the expanded rank structure. This new rank hierarchy of virus taxonomy will stimulate further research on virus origins and evolution, and vice versa, and could promote crosstalk with the taxonomies of cellular organisms.
Prevalence and speciation of brucellosis in febrile patients from a pastoralist community of Tanzania
Authors: Bodenham Rebecca F. , Lukambagire AbdulHamid S. , Ashford Roland T. , Buza Joram J. , Cash-Goldwasser Shama , Crump John A. , Kazwala Rudovick R. , Maro Venance P. , McGiven John , Mkenda Nestory , Mmbaga Blandina T. , Rubach Matthew P. , Sakasaka Philoteus , Shirima Gabriel M. , Swai Emanuel S. , Thomas Kate M. , Whatmore Adrian M. , Haydon Daniel T. , Halliday Jo E. B. 
Published: April 2020

AbstractBrucellosis is an endemic zoonosis in sub-Saharan Africa. Pastoralists are at high risk of infection but data on brucellosis from these communities are scarce. The study objectives were to: estimate the prevalence of human brucellosis, identify the Brucella spp. causing illness, describe non-Brucella bloodstream infections, and identify risk factors for brucellosis in febrile patients from a pastoralist community of Tanzania. Fourteen (6.1%) of 230 participants enrolled between August 2016 and October 2017 met study criteria for confirmed (febrile illness and culture positivity or ≥four-fold rise in SAT titre) or probable (febrile illness and single SAT titre ≥160) brucellosis. Brucella spp. was the most common bloodstream infection, with B. melitensis isolated from seven participants and B. abortus from one. Enterococcus spp., Escherichia coli, Salmonella enterica, Staphylococcus aureus and Streptococcus pneumoniae were also isolated. Risk factors identified for brucellosis included age and herding, with a greater probability of brucellosis in individuals with lower age and who herded cattle, sheep or goats in the previous 12 months. Disease prevention activities targeting young herders have potential to reduce the impacts of human brucellosis in Tanzania. Livestock vaccination strategies for the region should include both B. melitensis and B. abortus.
Multiband entropy-based feature-extraction method for automatic identification of epileptic focus based on high-frequency components in interictal iEEG
Authors: Akter Most. Sheuli , Islam Md. Rabiul , Iimura Yasushi , Sugano Hidenori , Fukumori Kosuke , Wang Duo , Tanaka Toshihisa , Cichocki Andrzej 
Published: April 2020

AbstractPresurgical investigations for categorizing focal patterns are crucial, leading to localization and surgical removal of the epileptic focus. This paper presents a machine learning approach using information theoretic features extracted from high-frequency subbands to detect the epileptic focus from interictal intracranial electroencephalogram (iEEG). It is known that high-frequency subbands (>80 Hz) include important biomarkers such as high-frequency oscillations (HFOs) for identifying epileptic focus commonly referred to as the seizure onset zone (SOZ). In this analysis, the multi-channel interictal iEEG signals were splitted into segments and each segment was decomposed into multiple high-frequency subbands. The different types of entropy were calculated for each of the subbands and the sparse linear discriminant analysis (sLDA) was applied to select the prominent entropy features. Due to the imbalance of SOZ and non-SOZ channels in iEEG data, the use of machine learning techniques is always tricky. To deal with the imbalanced learning problem, an adaptive synthetic oversampling approach (ADASYN) with radial basis function kernel-based SVM was used to detect the focal segments. Finally, the epileptic focus was identified based on detection of focal segments on SOZ and non-SOZ channels. Eight patients were examined to observe the efficiency of the automatic detector. The experimental results and statistical tests indicate that the proposed automatic detector can identify the epileptic focus accurately and efficiently.