bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting seabird responses to invasive species eradication
Authors: Bird Jeremy P. , Fuller Richard A. , Terauds Aleks , McInnes Julie C. , Pascoe Penelope P. , Travers Toby D. , Alderman Rachael , Shaw Justine D. 
Published: April 2021

ABSTRACTMaximising survey efficiency can help reduce the trade-off between spending limited conservation resources on evaluating performance of past interventions and directing those resources towards future interventions. Seabird responses to island eradications are often poorly evaluated owing to financial, logistical and methodological challenges associated with remote field work and species ecology. We surveyed an assemblage of threatened seabirds following the world’s largest island eradication of multiple invasive species, testing multiple survey designs and outputs. We compared the outcomes of two important choices made during survey design: 1) whether to use unbiased or targeted surveys; and 2) implementing design-based or model-based analyses. An unbiased whole-island stratified randomised survey design performed well in terms of confidence in the final population estimates for widespread species, but poorly for localised recolonising species. For widespread species, model-based analyses resulted in slightly lower population estimates with narrower confidence intervals than traditional design-based approaches but failed to capture the realised niches of recolonising species, resulting in population estimates three orders of magnitude higher than current best estimates. We conclude that a multi-method approach to survey design best captures the size and distribution of recovering populations when the study system is ecologically diverse—importantly our results suggest there is no single strategy for efficient surveys of diverse seabird communities following large island invasive species eradications.
Rapid, but limited, zooplankton adaptation to simultaneous warming and acidification
Authors: Dam Hans G. , deMayo James A. , Park Gihong , Norton Lydia , He Xuejia , Finiguerra Michael B. , Baumann Hannes , Brennan Reid S. , Pespeni Melissa H. 
Published: April 2021

AbstractPredicting the response of marine metazoans to climate change is hampered by a lack of studies on evolutionary adaptation, particularly to combined ocean warming and acidification (OWA). We provide evidence for rapid adaptation to OWA in the foundational copepod species,Acartia tonsa, by assessing changes in population fitness based on a comprehensive suite of life-history traits, using an orthogonal experimental design of nominal temperature (18°C, 22°C) andpCO2(400, 2000 μatm) for 25 generations (~1 year). Egg production and hatching success initially decreased under OWA, resulting in a 56% reduction in fitness. However, both traits recovered by the third generation and average fitness was reduced thereafter by only 9%. Antagonistic interactions between warming and acidification in later generations decreased survival, thereby limiting full fitness recovery. Our results suggest such interactions constrain evolutionary rescue and add complexity to predictions of the responses of metazoan populations to climate change.
ATP dependent polymerization dynamics of bacterial actin proteins involved inSpiroplasmaswimming
Authors: Takahashi Daichi , Fujiwara Ikuko , Sasajima Yuya , Narita Akihiro , Imada Katsumi , Miyata Makoto 
Published: April 2021

AbstractMreB is a bacterial protein belonging to the actin superfamily. It polymerises into an antiparallel double-stranded filament that generally functions in cell shape determination by maintaining cell wall synthesis.Spiroplasma eriocheiris, a helical wall-less bacterium, has five classes of MreB homologs (SpeMreB1-5) that are likely to be involved in swimming motility. Here, we investigated the structure, ATPase activity, and polymerisation dynamics of SpeMreB3 and SpeMreB5. SpeMreB3 polymerised into an antiparallel double-stranded filament, and SpeMreB5 formed sheets, including the antiparallel filament, upon the binding of a nucleotide. SpeMreB3 showed slow Pirelease owing to the lack of an amino acid motif conserved in the catalytic centre of MreB family proteins. Our crystal structures of SpeMreB3 and analyses of the mutant variants showed that the amino acid motif most likely plays a role in eliminating the proton of the nucleophilic water for ATP hydrolysis. Our sedimentation assay suggests that SpeMreB3 has a lower polymerisation activity than SpeMreB5, while their polymerisation dynamics are qualitatively similar to those of other actin superfamily proteins, in which ATP hydrolysis stabilises the filament, and Pirelease leads to depolymerisation.
RAMPs regulate signalling bias and internalisation of the GIPR
Authors: Harris Matthew , Mackie Duncan I. , Pawlak John B. , Carvalho Sabrina , Truong Tin T. , Safitri Dewi , Yeung Ho Yan , Routledge Sarah , Harper Matthew T. , Al-Zaid Bashaier , Soave Mark , Al-Sabah Suleiman , Inoue Asuka , Poyner David R. , Hill Stephen J. , Briddon Stephen J. , Sexton Patrick M. , Wootten Denise , Zhao Peishen , Caron Kathleen M. , Ladds Graham 
Published: April 2021

AbstractGastric inhibitory polypeptide (GIP) receptor is a class B1 GPCR, that responds to GIP and physiologically potentiates glucose-stimulated insulin secretion. Like most class B1 GPCRs, GIPR has been shown to interact with RAMPs, yet the effects of RAMPs on its signalling and trafficking remain poorly understood. We demonstrate that RAMPs modulate G protein activation and GIPR internalisation profiles. RAMP3 reduced GIPR Gsactivation and cAMP production but retained GIPR at the cell surface, and this was associated with prolonged ERK1/2 phosphorylation and β-arrestin association. By contrast, RAMP1/2 reduced Gq/11/15activation of the GIPR. Through knockout mice studies, we show that RAMP1 is important to the normal physiological functioning of GIPR to regulate blood glucose levels. Thus, RAMPs act on G protein/β-arrestin complexes, having both acute and chronic effects on GIPR function, while this study also raises the possibility of a more general role of RAMP3 to enhance GPCR plasma membrane localisation.
The Polar Night Shift: Annual Dynamics and Drivers of Microbial Community Structure in the Arctic Ocean
Authors: Wietz Matthias , Bienhold Christina , Metfies Katja , Torres-Valdés Sinhué , von Appen Wilken-Jon , Salter Ian , Boetius Antje 
Published: April 2021

ABSTRACTChange is a constant in the Arctic Ocean, with extreme seasonal differences in daylight, ice cover and temperature. The biodiversity and ecology of marine microbes across these extremes remain poorly understood. Here, using an array of autonomous samplers and sensors, we portray an annual cycle of microbial biodiversity, nutrient budgets and oceanography in the major biomes of the Fram Strait. In the ice-free West Spitsbergen Current, community turnover followed the solar cycle, with distinct separation of a productive summer state dominated by diatoms and carbohydrate-degrading bacteria, and a regenerative winter state dominated by heterotrophic Syndiniales, radiolarians, chemoautotrophic bacteria and archaea. Winter mixing of the water column replenishing nitrate, phosphate and silicate, and the onset of light were the major turning points. The summer succession ofPhaeocystis, GrammonemaandThalassiosiracoincided with ephemeral peaks ofFormosa, Polaribacterand NS clades, indicating metabolic relationships between phytoplankton and bacteria. In the East Greenland Current, ice cover and greater sampling depth coincided with weaker seasonality, featuring weaker bloom/decay events and an ice-related winter microbiome. Low ice cover and advection of Atlantic Water coincided with diminished abundances of chemoautotrophic bacteria whilePhaeocystisandFlavobacteriaceaeincreased, suggesting that Atlantification alters phytoplankton diversity and the biological carbon pump. Our findings promote the understanding of microbial seasonality in Arctic waters, illustrating the ecological importance of the polar night and providing an essential baseline of microbial dynamics in a region severely affected by climate change.
A Comparison of Persistence of SARS-CoV-2 Variants on Stainless Steel
Authors: Pottage Thomas , Garratt Isobel , Onianwa Okechukwu , Spencer Antony , Paton Susan , Dunning Jake , Bennett Allan 
Published: April 2021

SummaryThe survival of newer variants of SARS-CoV-2 on a representative surface has been compared to the established UK circulating isolate to determine whether enhanced environmental stability could play a part in their increased transmissibility. Stainless-steel coupons were inoculated with liquid cultures of the three variants, with coupons recovered over seven days and processed for recoverable viable virus using plaque assay. After drying, there was no significant difference in inactivation rates between variants. Indicating there is no increased environmental persistence from the new variants.
Polymersomes decorated with SARS-CoV-2 spike protein receptor binding domain elicit robust humoral and cellular immunity
Authors: Volpatti Lisa R. , Wallace Rachel P. , Cao Shijie , Raczy Michal M. , Wang Ruyi , Gray Laura T. , Alpar Aaron T. , Briquez Priscilla S. , Mitrousis Nikolaos , Marchell Tiffany M. , Sasso Maria Stella , Nguyen Mindy , Mansurov Aslan , Budina Erica , Solanki Ani , Watkins Elyse A. , Schnorenberg Mathew R. , Tremain Andrew C. , Reda Joseph W. , Nicolaescu Vlad , Furlong Kevin , Dvorkin Steve , Yu Shann S. , Manicassamy Balaji , LaBelle James L. , Tirrell Matthew V. , Randall Glenn , Kwissa Marcin , Swartz Melody A. , Hubbell Jeffrey A. 
Published: April 2021

ABSTRACTA diverse portfolio of SARS-CoV-2 vaccine candidates is needed to combat the evolving COVID-19 pandemic. Here, we developed a subunit nanovaccine by conjugating SARS-CoV-2 Spike protein receptor binding domain (RBD) to the surface of oxidation-sensitive polymersomes. We evaluated the humoral and cellular responses of mice immunized with these surface-decorated polymersomes (RBDsurf) compared to RBD-encapsulated polymersomes (RBDencap) and unformulated RBD (RBDfree), using monophosphoryl lipid A-encapsulated polymersomes (MPLA PS) as an adjuvant. While all three groups produced high titers of RBD-specific IgG, only RBDsurf elicited a neutralizing antibody response to SARS-CoV-2 comparable to that of human convalescent plasma. Moreover, RBDsurf was the only group to significantly increase the proportion of RBD-specific germinal center B cells in the vaccination-site draining lymph nodes. Both RBDsurf and RBDencap drove similarly robust CD4+ and CD8+ T cell responses that produced multiple Th1-type cytokines. We conclude that multivalent surface display of Spike RBD on polymersomes promotes a potent neutralizing antibody response to SARS-CoV-2, while both antigen formulations promote robust T cell immunity.
The impact of incongruence and exogenous gene fragments on estimates of the eukaryote root
Authors: Al Jewari Caesar , Baldauf Sandra L. 
Published: April 2021

AbstractPhylogenomics uses multiple genetic loci to reconstruct evolutionary trees, under the stipulation that all combined loci share a common phylogenetic history,i.e., they are congruent. Congruence is primarily evaluated via single-gene trees, but these trees invariably lack sufficient signal to resolve deep nodes making it difficult to assess congruence at these levels. Two methods were developed to systematically assess congruence in multi-locus data. Protocol 1 uses gene jackknifing to measure deviation from a central mean to identify taxon-specific incongruencies in the form of persistent outliers. Protocol_2 assesses congruence at the sub-gene level using a sliding window. Both protocols were tested on a controversial data set of 76 mitochondrial proteins previously used in various combinations to assess the eukaryote root. Protocol_1 showed a concentration of outliers in under-sampled taxa, including the pivotal taxon Discoba. Further analysis of Discoba using Protocol_2 detected a surprising number of apparently exogenous gene fragments, some of which overlap with Protocol_1 outliers and others that do not. Phylogenetic analyses of the full data using the static LG-gamma evolutionary model support a neozoan-excavate root for eukaryotes (Discoba sister), which rises to 99-100% bootstrap support with data masked according to either Protocol_1 or Protocol_2. In contrast, site-heterogeneous (mixture) models perform inconsistently with these data, yielding all three possible roots depending on presence/absence/type of masking and/or extent of missing data. The neozoan-excavate root places Amorphea (including animals and fungi) and Diaphoretickes (including plants) as more closely related to each other than either is to Discoba (Jakobida, Heterolobosea, and Euglenozoa), regardless of the presence/absence of additional taxa.
The impact of viral mutations on recognition by SARS-CoV-2 specific T-cells
Authors: de Silva Thushan I. , Liu Guihai , B Lindsey Benjamin , Dong Danning , Shah Dhruv , J. Mentzer Alexander , Angyal Adrienn , Brown Rebecca , D. Parker Matthew , Ying Zixi , Yao Xuan , Turtle Lance , Dunachie Susanna ,   COVID-19 Genomics UK (COG-UK) Consortium, K. Maini Mala , Ogg Graham , Knight Julian C. , Peng Yanchun , Rowland-Jones Sarah L. , Dong Tao 
Published: April 2021

AbstractWe identify amino acid variants within dominant SARS-CoV-2 T-cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T-cells assessed by IFN-γ and cytotoxic killing assays. These data demonstrate the potential for T-cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T-cell as well as humoral immunity.
The causal role of transcranial alternating current stimulation at alpha frequency in boosting visual perceptual learning
Authors: He Qing , Yang Xin-Yue , Gong Baoqi , Bi Keyan , Fang Fang 
Published: April 2021

AbstractExtensive training improves our ability to perceive visual contents around us, a phenomenon known as visual perceptual learning (VPL). Numerous studies have been conducted to understand the mechanisms of VPL, while the neural oscillatory mechanisms underpinning VPL has yet to be elucidated. To this end, we adopted transcranial alternating current stimulation (tACS), a neuromodulatory technique that can alter ongoing brain rhythms in a frequency-specific manner by applying external weak electric fields, to stimulate targeted cortical areas in human subjects while they performed an orientation discrimination learning task. Five groups of subjects undertook five daily training sessions to execute the task. Four groups received occipital tACS stimulation at 10 Hz (alpha band), 20 Hz (beta band), 40 Hz (gamma band), or sham 10 Hz (sham), and one group was stimulated at the sensorimotor regions by 10 Hz tACS. Compared with the sham stimulation, occipital tACS at 10 Hz, but not at 20 Hz or 40 Hz, increased both the learning rate and performance improvement. However, when 10 Hz tACS was delivered to the sensorimotor areas, the modulatory effects of tACS were absent, suggesting that tACS modulated the orientation discrimination learning in a frequency- and location-specific manner. Moreover, the tACS-induced enhancement lasted at least two months after the termination of training. Our findings provide strong evidence for the causal role of alpha oscillations in VPL and shed new light on the design of effective neuromodulation protocols that might facilitate rehabilitation for patients with neuro-ophthalmological disorders.Significance StatementPerformance of visual tasks can be enhanced substantially by training, which is known as visual perceptual learning (VPL). However, little is known about the neural oscillatory mechanisms underlying VPL. To probe the causal link between a given oscillatory frequency band and VPL, transcranial alternating current stimulation (tACS) was applied while subjects performed an orientation discrimination learning task. Our results revealed that tACS modulates VPL in a frequency- and location-specific manner. Specifically, only training coupled with 10 Hz tACS over the occipital cortex speeded up the learning process and amplified the performance gain. Our findings demonstrate the causal role of alpha oscillations in VPL, and provide insight into developing more effective and efficient remediation protocols for clinical applications, e.g., amblyopia.
Functionalizing cell-free systems with CRISPR-associated proteins: Application to RNA-based circuit engineering
Authors: Lehr François-Xavier , Kuzembayeva Alina , Bailey Megan E. , Kleindienst Werner , Kabisch Johannes , Koeppl Heinz 
Published: April 2021

AbstractCell-free systems have become a compelling choice for the prototyping of synthetic circuits. Many robust protocols for preparing cell-free systems are now available along with toolboxes designed for a variety of applications. Thus far the production of cell-free extracts has often been decoupled from the production of functionalized proteins. Here, we leveraged the most recently published protocol for E. coli-based cell extracts with the endogenous production of two CRISPR-associated proteins, Csy4 and dCas9. We found pre-expression did not affect the resulting extract performance, and the final concentrations of the endonucleases matched the level required for synthetic circuit prototyping. We demonstrated the benefits and versatility of dCas9 and Csy4 through the use of RNA circuitry based on a combination of single guide RNAs, small transcriptional activator RNAs and toehold switches. For instance, we show that Csy4 processing increased fourfold the dynamic range of a previously published AND-logic gate. Additionally, blending the CRISPR-enhanced extracts enabled us to reduce leakage in a multiple inputs gate, and to extend the type of Boolean functions available for RNA-based circuits, such as NAND-logic. Finally, the use of dual transcriptional and translational reporters for the engineering of RNA-based circuits, allowed us to gain better insight into their underlying mechanisms. We hope this work will facilitate the adoption of advanced processing tools for RNA-based circuit prototyping in a cell-free environment.
Transient demographic approaches can drastically expand the toolbox of coral reef science
Authors: Cant James , Salguero-Gómez Roberto , Beger Maria 
Published: April 2021

AbstractCoral communities are threatened by an increasing plethora of abiotic and biotic disturbances. Preventing the ensuing loss of coral coverage and diversity calls for a mechanistic understanding of resilience across coral species and populations that is currently lacking in coral reef science. Assessments into the dynamics of coral populations typically focus on their long-term (i.e. asymptotic) characteristics, tacitly assuming stable environments in which populations can attain their long-term characteristics. Instead, we argue that greater focus is needed on investigating thetransient(i.e.short-term) dynamics of coral populations to describe and predict their characteristics and trajectories within unstable environments. Applying transient demographic approaches to the evaluation and forecasting of the responses of coral populations to disturbance holds promise for expediting our capacity to predict and manage the resilience of coral populations, species, and communities.
Inhibition of LipopolysaccharideE. coli-induced acute lung injury by extractedAntidesma bunius(L.) Spreng fruits as compared to Fluticasone Propionate, a corticosteroid
Authors: Muñoz Maria Nilda M. , Lucero Jennifer , Benzon Kimberly Stacy Hope , Reyes Jerica Isabel L. , de Silva Charina , Delicana Reuel C. , Tejada Urdujah A. , Chatterjee Swapan , Watanabe Kozo 
Published: April 2021

AbstractThe hallmark of Acute Lung Injury/Acute Respiratory Distress Syndrome (ALI/ARDS) is inflammation-induced alveolar-vascular barrier destruction and neutrophilic infiltration that leads to the formation of cytokines and oxygen radicals. The objective of the study is to investigate the protective and toxicological effects ofAntidesma bunius(L.) Spreng [Bignay] in murine model of LipopolysaccharideE. coli(LPS)-induced ALI and compared with Fluticasone Propionate (FP), a synthetic corticosteroid. We showed that extracted Bignay fruits have high amount of phenols, steroids and flavonoids but insignificant amount of heavy metals and aflatoxins. BALB/c mice of either sex were divided into 4 groups in the ALI mouse model; Group 1: vehicle control; Group 2: LPS alone; Group 3: Bignay + LPS; and Group 4: FP + LPS. Bignay and FP were administered via intraperitoneal injection while LPS was given intra-tracheally. Biomarkers of ALI such as total lung inflammatory cell count, total lung protein content, lung edema and interleukin-6 (IL-6) secretion were measured 24 hrs after vehicle control or LPS treatment. Compared to vehicle controls, LPS caused significant increased in all measured biomarkers of ALI in samples collected from bronchoalveolar lavage fluid and were significantly attenuated by Bignay fruit extract or FP. Pulmonary vascular leakage caused by LPS was also evaluated after injection with Evans blue dye, an indication of lung injury. Extracted Bignay fruits or FP when given to mice 2 hrs after LPS administration substantially decreased the pulmonary vascular leak. Our findings are the first evidence demonstrating the preventive and non-toxic effects of extracted Bignay fruits in a murine model of LPS-induced ALI. The results could be attributed to the presence of active secondary metabolites such as flavonoids, phenols and steroids. It is also evident that extracted Bignay fruits are as effective as FP, well-established steroid, in blocking the biomarkers of ALI caused by LPS.
Genome-wide survey of the F-box/Kelch (FBK) members and molecular identification of a novel FBK geneTaAFRin wheat
Authors: Wei Chunru , Zhao Weiquan , Fan Runqiao , Meng Yuyu , Yang Yiming , Wang Xiaodong , Foroud Nora A. , Liu Daqun , Yu Xiumei 
Published: April 2021

AbstractF-box proteins play critical roles in plant responses to biotic/abiotic stresses. In the present study, a total of 68 wheat F-box/Kelch (TaFBK) gene sequences encoding for 74 proteins were obtained in a genome-wide survey against EnsemblPlants. The 74 TaFBK proteins were divided into 5 categories based on their domain structures. The FBK proteins from wheat, Arabidopsis, and three other cereal species were grouped into 7 clades, and the number of Kelch domains present was their key clustering criterion. Sixty-eightTaFBKgenes were unevenly distributed on 21 chromosomes. Most of TaFBKs were predicted to localize in the nucleus and cytoplasm.In silicoanalysis of a digital PCR revealed thatTaFBKswere expressed at multiple developmental stages and tissues, and in response to drought and/or heat stresses. TheTaFBK19gene, a homologous to theAttenuated Far-Red Response(AFR) genes in other plant species, and hence namedTaAFR, was selected for further analysis. The gene was isolated from the wheat line TcLr15 and its expression evaluated by quantitative real-time PCR.TaAFRtranscripts were primarily detected in wheat leaves, and its expression was found to be regulated by various abiotic and biotic stresses as well as plant signaling hormones. Of particular interest,TaAFRexpression was differentially regulated in the compatiblevsincompatible wheat leaf rust reaction. Subcellular localization studies showed that TaAFR accumulates in the nucleus and cytoplasm. Three TaAFR-interacting proteins were identified experimentally: Skp1/ASK1-like protein (Skp1), ADP-ribosylation factor 2-like isoform X1 (ARL2) and phenylalanine ammonia-lyase (PAL). Further analysis revealed that the Skp1 protein interacted specifically with the F-box domain of TaAFR, while ARL2 and PAL were recognized by the Kelch domain. The data presented herein provides a solid foundation from which the function and metabolic network of TaAFR and other wheat FBKs can be further explored.