bluuebunny/crossref_metadata_2025_split huggingface dataset:
Poor availability of context-specific evidence hampers decision-making in conservation
Authors: Christie Alec P. , Amano Tatsuya , Martin Philip A. , Petrovan Silviu O. , Shackelford Gorm E. , Simmons Benno I. , Smith Rebecca K. , Williams David R. , Wordley Claire F. R. , Sutherland William J. 
Published: February 2020

AbstractEvidence-based conservation relies on robust and relevant evidence. Practitioners often prefer locally relevant studies whose results are more likely to be transferable to the context of planned conservation interventions. To quantify the availability of relevant evidence for amphibian and bird conservation we reviewed Conservation Evidence, a database of quantitative tests of conservation interventions. Studies were geographically clustered and found at extremely low densities - fewer than one study was present within a 2,000 km radius of a given location. The availability of relevant evidence was extremely low when we restricted studies to those studying biomes or taxonomic orders containing high percentages of threatened species, compared to the most frequently studied biomes and taxonomic orders. Further constraining the evidence by study design showed that only 17-20% of amphibian and bird studies used robust designs. Our results highlight the paucity of evidence on the effectiveness of conservation interventions, and the disparity in evidence for local contexts that are frequently studied and those where conservation needs are greatest. Addressing the serious global shortfall in context-specific evidence requires a step change in the frequency of testing conservation interventions, greater use of robust study designs and standardized metrics, and methodological advances to analyze patchy evidence bases.
Integrative analyses to investigate the link between microbial activity and metabolites degradation during anaerobic digestion
Authors: Cardona Laetitia , Lê Cao Kim Anh , Puig-Castellví Francesc , Bureau Chrystelle , Madigou Céline , Mazéas Laurent , Chapleur Olivier 
Published: February 2020

AbstractAnaerobic digestion (AD) is a promising biological process which converts waste into sustainable energy. To fully exploit AD’s capability, we need to deepen our knowledge of the microbiota involved in this complex bioprocess. High-throughput methodologies open new perspectives to investigate AD process at the molecular level, supported by recent data integration methodologies to extract relevant information. In this study, we investigated the link between microbial activity and substrate degradation in a lab-scale anaerobic co-digestion experiment, where bioreactors were fed with 9 different mixtures of three co-substrates (fish waste, sewage sludge, and grass). Samples were profiled using 16S rRNA sequencing and untargeted metabolomics. In this article, we propose a suite of multivariate tools to statistically integrate these data and identify coordinated patterns between groups of microbial and metabolic profiles specific of each co-substrate. Five main groups of features were successfully evidenced, including cadaverine degradation found to be associated with the activity of microorganisms from the orderClostridialesand the genusMethanosarcina. This study highlights the potential of data integration towards a comprehensive understanding of AD microbiota.
Efficient Immune Cell Genome Engineering with Improved CRISPR Editing Tools
Authors: Chan Waipan , Gottschalk Rachel A. , Yao Yikun , Pomerantz Joel L. , Germain Ronald N. 
Published: February 2020

AbstractCRISPR (clustered regularly interspaced short palindromic repeats)-based methods have revolutionized genome engineering and the study of gene-phenotype relationships. However, modifying cells of the innate immune system, especially macrophages, has been challenging because of cell pathology and low targeting efficiency resulting from nucleic acid activation of sensitive intracellular sensors. Likewise, lymphocytes of the adaptive immune system are largely refractory to CRISPR-enhanced homology-directed repair (HDR) due to inefficient or toxic delivery of donor templates via transient transfection methods. To overcome these challenges and limitations, we developed three improved methods for CRISPR-based genome editing using a hit-and-run transient expression strategy to minimize off-target effects and generate more precise genome editing. Overall, our enhanced CRISPR tools and strategies designed to tackle both murine and human immune cell genome engineering are expected to be widely applicable not only in hematopoietic cells but also other mammalian cell types of interest.All animal experiments were done in accordance with the guidelines of the NIAID/NIH Institutional Animal Care and Use Committee.
Reversal of β-amyloid induced microglial toxicityin vitroby activation of Fpr2/3
Authors: Wickstead Edward S. , Karim Husnain A. , Manuel Roberta E. , Biggs Christopher , Getting Stephen J. , McArthur Simon 
Published: February 2020

AbstractBackground and PurposeMicroglial inflammatory activity is thought to be a major contributor to the pathology of neurodegenerative conditions such as Alzheimer’s disease (AD), and strategies to restrain their behaviour are under active investigation. Classically, anti-inflammatory approaches aim to suppress pro-inflammatory mediator production, but exploitation of inflammatory resolution, the endogenous process whereby an inflammatory reaction is terminated, has not been fully investigated as a therapeutic approach in AD. In this study, we sought to provide proof-of-principal that the major pro-resolving actor, formyl peptide receptor 2, Fpr2, could be targeted to reverse microglial activation induced by the AD-associated pro-inflammatory stimulus, oligomeric β-amyloid (oAβ).Experimental ApproachThe immortalised murine microglial cell line BV2 was employed as a model system to investigate the pro-resolving effects of the Fpr2 ligand QC1 upon oAβ-induced inflammatory, oxidative and metabolic behaviour. Cytotoxic behaviour of BV2 cells was assessed through use of co-cultures with retinoic acid-differentiated human SH-SY5Y cells.Key ResultsStimulation of BV2 cells with oAβ at 100nM did not induce classical inflammatory marker production but did stimulate production of reactive oxygen species (ROS), an effect that could be reversed by subsequent treatment with the Fpr2 ligand QC1. Further investigation revealed that oAβ-induced ROS production was associated with NADPH oxidase activation and a shift in BV2 cell metabolic phenotype, activating the pentose phosphate pathway and NADPH production, changes that were again reversed by QC1 treatment. Microglial oAβ-stimulated ROS production was sufficient to induce apoptosis of bystander SH-SY5Y cells, an effect that could be prevented by QC1 treatment.Conclusion and ImplicationsIn this study, we provide proof-of-concept data that indicate exploitation of the pro-resolving receptor Fpr2 can reverse damaging oAβ-induced microglial activation. Future strategies aiming to restrain neuroinflammation in conditions such as AD should examine pro-resolving actors as a mechanism to harness the brain’s endogenous healing pathways and limit neuroinflammatory damage.
Slightly beneficial genes are retained by evolving Horizontal Gene Transfer despite selfish elements
Authors: van Dijk B. , Hogeweg P. , Doekes H.M. , Takeuchi N. 
Published: February 2020

AbstractHorizontal gene transfer (HGT) is a key component of bacterial evolution, which in concert with gene loss can result in rapid changes in gene content. While HGT can evidently aid bacteria to adapt to new environments, it also carries risks since bacteria may pick up selfish genetic elements (SGEs). Here, we use modeling to study how bacterial growth rates are affected by HGT of slightly beneficial genes, if bacteria can evolve HGT to improve their growth rates, and when HGT is evolutionarily maintained in light of harmful SGEs. We find that we can distinguish between four classes of slightly beneficial genes: indispensable, enrichable, rescuable, and unrescuable genes. Rescuable genes – genes that confer small fitness benefits and are lost from the population in the absence of HGT — can be collectively retained by a bacterial community that engages in HGT. While this ‘gene-sharing’ cannot evolve in well-mixed cultures, it does evolve in a spatially structured population such as a biofilm. Although HGT does indeed enable infection by harmful SGEs, HGT is nevertheless evolutionarily maintained by the hosts, explaining the stable coexistence and co-evolution of bacteria and SGEs.
A universal subcuticular bacterial symbiont of a coral predator, the crown-of-thorns starfish, in the Indo-Pacific
Authors: Wada Naohisa , Yuasa Hideaki , Kajitani Rei , Gotoh Yasuhiro , Ogura Yoshitoshi , Yoshimura Dai , Toyoda Atsushi , Tang Sen-Lin , Higashimura Yukio , Sweatman Hugh , Forsman Zac , Bronstein Omri , Eyal Gal , Thongtham Nalinee , Itoh Takehiko , Hayashi Tetsuya , Yasuda Nina 
Published: February 2020

AbstractBackgroundPopulation outbreaks of the crown-of-thorns starfish (Acanthaster plancisensu lato; COTS), a primary predator of reef-building corals in the Indo-Pacific Ocean, are major concerns in coral reef management. While biological and ecological knowledge of COTS has been accumulating since the 1960s, little is known about its associated bacteria. The aim of this study was to provide fundamental information on dominant COTS-associated bacteria through a multifaceted molecular approach.MethodsA total of 205 COTS individuals from 17 locations throughout the Indo-Pacific Ocean were examined for the presence of COTS-associated bacteria. We conducted 16S rRNA metabarcoding of COTS to determine the bacterial profiles of different parts of the body, and generated a full-length 16S rRNA gene sequence from a single dominant bacterium, which we designated COTS27. We performed phylogenetic analysis to determine the taxonomy, screening of COTS27 across the Indo-Pacific, FISH to visualize it within the COTS tissues, and reconstruction of the chromosome from the hologenome sequence data.ResultsWe discovered that a single bacterium exists at high densities in the subcuticular space in COTS forming a biofilm-like structure between the cuticle and the epidermis. COTS27 belongs to a clade that presumably represents a distinct order (so-called marine spirochetes) in the phylumSpirochaetesand is universally present in COTS throughout the Indo-Pacific Ocean. The reconstructed genome of COTS27 includes some genetic traits that are probably linked to adaptation to marine environments and evolution as an extracellular endosymbiont in subcuticular spaces.ConclusionsCOTS27 can be found in three allopatrically speciated COTS species, ranging from northern Red Sea to the Pacific, implying that symbiotic relationship arose before the speciation (approximately 2 million years ago). The universal association of COTS27 with COTS and nearly mono-specific association at least with the Indo-Pacific COTS potentially provides a useful model system for studying symbiont-host interactions in marine invertebrates.
Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction
Authors: Ranjan Anand , Nguyen Vu Q. , Liu Sheng , Wisniewski Jan , Kim Jee Min , Tang Xiaona , Mizuguchi Gaku , Elalaoui Ejlal , Nickels Timothy J. , Jou Vivian , English Brian P. , Zheng Qinsi , Luk Ed , Lavis Luke D. , Lionnet Timothee , Wu Carl 
Published: February 2020

AbstractThe H2A.Z histone variant, a genome-wide hallmark of permissive chromatin, is enriched near transcription start sites in all eukaryotes. H2A.Z is deposited by the SWR1 chromatin remodeler and evicted by unclear mechanisms. We tracked H2A.Z in living yeast at single-molecule resolution, and found that H2A.Z eviction is dependent on RNA Polymerase II (Pol II) and the Kin28/Cdk7 kinase, which phosphorylates Serine 5 of heptapeptide repeats on the carboxy-terminal domain of the largest Pol II subunit Rpb1. These findings link H2A.Z eviction to transcription initiation, promoter escape and early elongation activities of Pol II. Because passage of Pol II through +1 nucleosomes genome-wide would obligate H2A.Z turnover, we propose that global transcription of noncoding RNAs prior to premature termination, in addition to transcription of mRNAs, are responsible for eviction of H2A.Z. Such usage of yeast Pol II suggests a general mechanism coupling eukaryotic transcription to erasure of the H2A.Z epigenetic signal.
Distinct chemotactic behavior in the originalEscherichia coliK-12 depending on forward-and-backward swimming, not on run-tumble movements
Authors: Kinosita Yoshiaki , Ishida Tsubasa , Yoshida Myu , Ito Rie , Morimoto Yusuke V. , Goto Kazuki , Berry Richard M. , Nishizaka Takayuki , Sowa Yoshiyuki 
Published: February 2020

AbstractMost motile bacteria are propelled by rigid, helical, flagellar filaments and display distinct swimming patterns to explore their favorable environments.Escherichia colicells have a reversible rotary motor at the base of each filament. They exhibit a run-tumble swimming pattern, driven by switching of rotatory direction which causes polymorphic flagellar transformation. Here we report a novel swimming mode inE. coliATCC10798, which is one of the original K-12 clones. High-speed tracking of single ATCC10798 cells showed forward and backward swimming with an average turning angle of 150°. The flagellar helicity remained right-handed with a 1.3 μm pitch and 0.14 μm helix radius, which is assumed to be a curly type, regardless of motor switching; the flagella of ATCC10798 did not show polymorphic transformation. The torque and rotational switching of the motor was almost identical to theE. coliW3110 strain, which is a derivative of K-12 and a wild-type for chemotaxis. The single point mutation of N87K in FliC, one of the filament subunits, is critical to the change in flagellar morphology and swimming pattern, and lack of flagellar polymorphism.E. colicells expressing FliC(N87K) sensed ascending a chemotactic gradient in liquid but did not form rings on a semi-solid surface. Based on these findings, we propose a flagellar polymorphism-dependent migration mechanism in structured environments.
Interspike intervals within retinal spike bursts combinatorially encode multiple stimulus features
Authors: Ishii Toshiyuki , Hosoya Toshihiko 
Published: February 2020

AbstractNeurons in various regions of the brain generate spike bursts. While the number of spikes within a burst has been shown to carry information, information coding by interspike intervals (ISIs) is less well understood. In particular, a burst withkspikes hask−1 intraburst ISIs, and thesek−1 ISIs could theoretically encodek−1 independent values. In this study, we demonstrate that such combinatorial coding occurs for retinal bursts. By recording ganglion cell spikes from isolated salamander retinae, we found that intraburst ISIs encode oscillatory light sequences that are much faster than the light intensity modulation encoded by the number of spikes. When a burst has three spikes, the two intraburst ISIs combinatorially encode the amplitude and phase of the oscillatory sequence. Analysis of trial-to-trial variability suggested that intraburst ISIs are regulated by two independent mechanisms responding to orthogonal oscillatory components, one of which is common to bursts with different number of spikes. Therefore, the retina encodes multiple stimulus features by exploiting all degrees of freedom of burst spike patterns, i.e., the spike number and multiple intraburst ISIs.Author SummaryNeurons in various regions of the brain generate spike bursts. Bursts are typically composed of a few spikes generated within dozens of milliseconds, and individual bursts are separated by much longer periods of silence (∼hundreds of milliseconds). Recent evidence indicates that the number of spikes in a burst, the interspike intervals (ISIs), and the overall duration of a burst, as well as the timing of burst onset, encode information. However, it remains unknown whether multiple ISIs within a single burst encode multiple independent information contents. Here we demonstrate that such combinatorial ISI coding occurs for spike bursts in the retina. We recorded ganglion cell spikes from isolated salamander retinae stimulated with computer-generated movies. Visual response analyses indicated that multiple ISIs within a single burst combinatorially encode the phase and amplitude of oscillatory light sequences, which are different from the stimulus feature encoded by the spike number. The result demonstrates that the retina encodes multiple stimulus features by exploiting all degrees of freedom of burst spike patterns, i.e., the spike number and multiple intraburst ISIs. Because synaptic transmission in the visual system is highly sensitive to ISIs, the combinatorial ISI coding must have a major impact on visual information processing.
Long-term changes in kelp forests in an inner basin of the Salish Sea
Authors: Berry Helen D. , Mumford Thomas F. , Christiaen Bart , Dowty Pete , Calloway Max , Ferrier Lisa , Grossman Eric E. , VanArendonk Nathan R. 
Published: February 2020

AbstractUnderstanding the historical extent of biogenic habitats can provide insight into the nature of human impacts and inform restoration and conservation actions. Kelp forests form an important biogenic habitat that responds to natural and human drivers. Global concerns exist about threats to kelp forests, yet long term information is limited and research suggests that trends are geographically distinct. We examined distribution of the bull kelpNereocystis luetkeanaover 145 years in South Puget Sound (SPS), a semi-protected inner basin in a fjord estuary complex in the northeast Pacific Ocean. We synthesized 48 historical and modernNereocystissurveys and examined presence/absence within 1-km shoreline segments along 452 km of shoreline. Over the last 145 years,Nereocystishas been documented in 26% of the shoreline segments. Its extent decreased 62% basin-wide between the 1870s and 2017, with extreme losses in the two out of three sub-basins (96% in Central and 83% in West). In recent years, almost allNereocystisoccurred in the East sub-basin. In the majority of segments whereNereocystisdisappeared, the most recent observation was 4 decades ago, or earlier. Multiple natural and human factors that are known to impact kelp could have contributed to observed patterns, but limited data exist at the spatial and temporal scale of this study. In some areas, recent environmental conditions approached thresholds associated with decreased kelp performance. LongstandingNereocystislosses occurred exclusively in areas with relatively low current velocities. RemainingNereocystispredominantly occurred in areas where circulation is stronger. Exceptions to this pattern demonstrate that additional factors outside the scope of this study contributed to trajectories ofNereocystispersistence or loss.
Effects of MP2RAGE B1+sensitivity on inter-site T1reproducibility and morphometry at 7T
Authors: Haast Roy AM , Lau Jonathan C , Ivanov Dimo , Menon Ravi S , Uludağ Kâmil , Khan Ali R 
Published: February 2020

AbstractMost neuroanatomical studies are based on MR images, whose intensity profiles are not solely determined by the tissue’s longitudinal relaxation times (T1) but also affected by varying non-T1contributions, hampering data reproducibility. In contrast, quantitative imaging using the MP2RAGE sequence, for example, allows direct characterization of the brain based on the tissue property of interest. Combined with 7 Tesla (7T) MRI, this offers unique opportunities to obtain robust high-resolution brain data characterized by a high reproducibility, sensitivity and specificity. However, specific MP2RAGE parameters choices – e.g., to emphasize intracortical myelin-dependent contrast variations – can substantially impact image quality and cortical analyses through remnants of B1+-related intensity variations, as illustrated in our previous work. To follow up on this: we (1) validate this protocol effect using a dataset acquired with a particularly B1+insensitive set of MP2RAGE parameters combined with parallel transmission excitation; and (2) extend our analyses to evaluate the effects on hippocampal and subcortical morphometry. The latter remained unexplored initially but will provide important insights related to generalizability and reproducibility of neurodegenerative research using 7T MRI. We confirm that B1+inhomogeneities have a considerably variable effect on cortical T1and thickness estimates, as well as on hippocampal and subcortical morphometry depending on MP2RAGE setup. While T1differed substantially across datasets initially, we show inter-site T1comparability improves after correcting for the spatially varying B1+field using a separately acquired Sa2RAGE B1+map. Finally, as for cortical thickness, removal of B1+residuals affects hippocampal and subcortical volumetry and boundary definitions, particularly near structures characterized by strong intensity changes (e.g. cerebral spinal fluid and arteries). Taken together, we show that the choice of MP2RAGE parameters can impact T1comparability across sites and present evidence that hippocampal and subcortical segmentation results are modulated by B1+inhomogeneities. This calls for careful (1) consideration of sequence parameters when setting acquisition protocols; as well as (2) interpretation of results focused on neuroanatomical changes due to disease.HighlightsPreviously observed effects of B1+inhomogeneities on cortical T1and thickness depend strongly on MP2RAGE parametersInter-site comparability of cortical T1and thickness greatly improves after removal of B1+residualsPost-hoc MP2RAGE B1+correction affects hippocampal (and subcortical) size and shape analysesNeuroradiological research would benefit from careful examination of imaging protocols and their impact on results, especially when B1+maps are not acquired
Altered parasitism of a butterfly assemblage associated with a range-expanding species
Authors: Audusseau H. , Ryrholm N. , Stefanescu C. , Tharel S. , Jansson C. , Champeaux L. , Shaw M. R. , Raper C. , Lewis O. T. , Janz N. , Schmucki R. 
Published: February 2020

AbstractAimBiotic interactions are an important factor structuring ecological communities but data scarcity limits our understanding of the impact of their response to climate and land use changes on communities. We studied the impact of a change in species assemblage on biotic interactions in a community of closely-related butterflies. Specifically, we examined the impact of the recent range expansion ofAraschnia levanaon the resident species, with a particular focus on natural enemies, parasitoids, shared with other butterfly species in the assemblage.LocationSweden.Time periodTwo years (2017-2018).Major taxa studiedNettle-feeding butterflies (Aglais urticae, Aglais io, Araschnia levana, andVanessa atalanta) and their parasitoids.MethodsWe assessed parasitism in 6777 butterfly larvae sampled in the field from 19 sites distributed along a 500 km latitudinal gradient, and every two weeks throughout species’ reproductive seasons. We identified the parasitoid complex of each butterfly species and their overlap, and analysed how parasitism rates were affected by species assemblage, variations in abundance, time, and the arrival ofA. levana.ResultsParasitoids caused high mortality, with substantial overlap across the four host species. The composition of the host community influenced parasitism rates and this effect was specific to each species. In particular, the rate of parasitism in resident species was comparatively higher at sites whereA. levanahas been established for longer.Main conclusionsParasitoid pressure is a significant source of mortality in the nettle-feeding butterfly community studied. Variations in butterfly species assemblages are associated with substantial variations in rates of parasitism. This is likely to affect the population dynamics of their butterfly host species, and, potentially, the larger number of species with which they interact.