bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temperature increases soil respiration across ecosystem types and soil development, but soil properties determine the magnitude of this effect
Authors: Dacal Marina , Delgado-Baquerizo Manuel , Barquero Jesús , Berhe Asmeret Asefaw , Gallardo Antonio , Maestre Fernando T. , García-Palacios Pablo 
Published: October 2020

AbstractSoil carbon losses to the atmosphere, via soil heterotrophic respiration, are expected to increase in response to global warming, resulting in a positive carbon-climate feedback. Despite the well-known suite of abiotic and biotic factors controlling soil respiration, much less is known about how the magnitude of soil respiration responses to temperature changes over soil development and across contrasting soil properties. Here, we investigated the role of soil development stage and soil properties in driving the responses of soil heterotrophic respiration to increasing temperatures. We incubated soils from eight chronosequences ranging in soil age from hundreds to million years, and encompassing a wide range of vegetation types, climatic conditions, and chronosequences origins, at three assay temperatures (5, 15 and 25°C). We found a consistent positive effect of assay temperature on soil respiration rates across the eight chronosequences evaluated. However, soil properties such as organic carbon concentration, texture, pH, phosphorus content, and microbial biomass determined the magnitude of temperature effects on soil respiration. Finally, we observed a positive effect of soil development stage on soil respiration that did not alter the magnitude of assay temperature effects. Our work reveals that key soil properties alter the magnitude of the positive effect of temperature on soil respiration found across ecosystem types and soil development stages. This information is essential to better understand the magnitude of the carbon-climate feedback, and thus to establish accurate greenhouse gas emission targets.
Attack behaviour in naïve Gyrfalcons is modelled by the same guidance law as in Peregrines, but at a lower guidance gain
Authors: Brighton Caroline H. , Chapman Katherine E. , Fox Nicholas C. , Taylor Graham K. 
Published: October 2020

ABSTRACTThe aerial hunting behaviours of birds are strongly influenced by their flight morphology and ecology, but little is known of how this variation relates to the behavioural algorithms guiding flight. Here we use onboard GPS loggers to record the attack trajectories of captive-bred Gyrfalcons (Falco rusticolus) during their maiden flights against robotic aerial targets, which we compare to existing flight data from Peregrines (Falco peregrinus) The attack trajectories of both species are modelled most economically by a proportional navigation guidance law, which commands turning in proportion to the angular rate of the line-of-sight to target, at a guidance gainN. However, Gyrfalcons operate at significantly lower values ofNthan Peregrines, producing slower turning and a longer path to intercept. Gyrfalcons are less agile and less manoeuvrable than Peregrines, but this physical constraint is insufficient to explain their lower guidance gain. On the other hand, lower values ofNpromote the tail-chasing behaviour that is typical of wild Gyrfalcons, and which apparently serves to tire their prey in a prolonged high-speed pursuit. Moreover, during close pursuit of fast evasive prey such as Ptarmigan (Lagopusspp.), proportional navigation will be less prone to being thrown off by erratic target manoeuvres ifNis low. The fact that low-gain proportional navigation successfully models the maiden attack flights of Gyrfalcons suggests that this behavioural algorithm is embedded in a hardwired guidance loop, which we hypothesise is ancestral to the clade containing Gyrfalcons and Peregrines.SUMMARY STATEMENTNaïve Gyrfalcons attacking aerial targets are modelled by the same proportional navigation guidance law as Peregrines, but with a lower navigation constant that promotes tail-chasing rather than efficient interception.
Phosphorylation of the mitochondrial triphosphate tunnel metalloenzyme TTM1 regulates programmed cell death in senescence
Authors: Karia Purva , Yoshioka Keiko , Moeder Wolfgang 
Published: October 2020

ABSTRACTThe role of mitochondria in programmed cell death (PCD) during animal growth and development is well documented, but much less is known for plants. We previously showed that theArabidopsis thalianatriphosphate tunnel metalloenzyme (TTM) proteins TTM1 and TTM2 are tail-anchored proteins that localize in the mitochondrial outer membrane and participate in PCD during senescence and immunity, respectively. Here, we show that TTM1 is specifically involved in senescence induced by abscisic acid (ABA). Moreover, phosphorylation of TTM1 by multiple mitogen-activated protein kinases (MAPKs) regulates its function and turnover. A combination of proteomics andin vitrokinase assays revealed three major phosphorylation sites of TTM1 (S10, S437, and S490), which are phosphorylated upon perception of senescence cues such as ABA and prolonged darkness. S437 is phosphorylated by the MAP kinases MPK3 and MPK4, and S437 phosphorylation is essential for TTM1 function in senescence. These MPKs, together with three additional MAP kinases (MPK1, MPK7, and MPK6), phosphorylate S10 and S490, marking TTM1 for protein turnover, which likely prevents uncontrolled cell death. Taken together, our results show that multiple MPKs regulate the function and turnover of the mitochondrial protein TTM1 during senescence-related PCD, revealing a novel link between mitochondria and PCD.SummaryEmail addresses:purva.karia@mail.utoronto.ca
MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance
Authors: Nicholls Samuel M. , Poplawski Radoslaw , Bull Matthew J. , Underwood Anthony , Chapman Michael , Abu-Dahab Khalil , Taylor Ben , Jackson Ben , Rey Sara , Amato Roberto , Livett Rich , Gonçalves Sónia , Harrison Ewan M. , Peacock Sharon J. , Aanensen David M , Rambaut Andrew , Connor Thomas R. , Loman Nicholas J. ,   The COVID-19 Genomics UK (COG-UK) Consortium
Published: October 2020

AbstractGenomic epidemiology has become an increasingly common tool for epidemic response. Recent technological advances have made it possible to sequence genomes rapidly enough to inform outbreak response, and cheaply enough to justify dense sampling of even large epidemics. With increased availability of sequencing it is possible for agile networks of sequencing facilities to collaborate on the sequencing and analysis of epidemic genomic data.In response to the ongoing SARS-CoV-2 pandemic in the United Kingdom, the COVID-19 Genomics UK (COG-UK) consortium was formed with the aim of rapidly sequencing SARS-CoV-2 genomes as part of a national-scale genomic surveillance strategy. The network consists of universities, academic institutes, regional sequencing centres and the four UK Public Health Agencies.We describe the development and deployment of Majora, an encompassing digital infrastructure to address the challenge of collecting and integrating both genomic sequencing data and sample-associated metadata produced across the COG-UK network. The system was designed and implemented pragmatically to stand up capacity rapidly in a pandemic caused by a novel virus. This approach has underpinned the success of COG-UK, which has rapidly become the leading contributor of SARS-CoV-2 genomes to international databases and has generated over 60,000 sequences to date.
Evidence accumulation, not “self-control,” explains dorsolateral prefrontal activation during normative choice
Authors: Hutcherson Cendri A. , Tusche Anita 
Published: October 2020

AbstractWhat role do cognitive control regions like the dorsolateral prefrontal cortex (dlPFC) play in normative behavior (e.g., generosity, healthy eating)? Some models suggest that dlPFC activation during normative choice reflects the use of control to overcome default hedonistic preferences. Here, we develop an alternative account, showing that anattribute-based neural drift diffusion model (anDDM)predicts trial-by-trial variation in dlPFC response across three fMRI studies and two self-control contexts (altruistic sacrifice and healthy eating). Using the anDDM to simulate a variety of self-control dilemmas generated a novel prediction: although dlPFC activity mighttypicallyincrease for norm-consistent choices, deliberate self-regulation focused on normative goals shoulddecreaseor evenreversethis pattern (i.e., greater dlPFC response for hedonic, self-interested choices). We confirmed these predictions in both altruistic and dietary choice contexts. Our results suggest that dlPFC response during normative choice may depend more on value-based evidence accumulation than inhibition of our baser instincts.
Pescoids and chimeras to probe early evo-devo in the fishAstyanax mexicanus
Authors: Torres-Paz Jorge , Rétaux Sylvie 
Published: October 2020

AbstractThe fish speciesAstyanax mexicanuswith its sighted and blind eco-morphotypes has become an original model to challenge vertebrate developmental evolution. Recently, we demonstrated that phenotypic evolution can be impacted by early developmental events starting from the production of oocytes in the fish ovaries.A. mexicanusoffers an amenable model to test the influence of maternal effect on cell fate decisions during early development, yet the mechanisms by which the information contained in the eggs is translated into specific developmental programs remain obscure due to the lack of specific tools in this emergent model. Here we describe methods for the generation of gastruloids from yolkless-blastoderm explants to test the influence of embryonic and extraembryonic properties on cell fate decisions, as well as the production of chimeric embryos obtained by intermorph cell transplantations to probe cell autonomous or non-autonomous processes. We show thatAstyanaxgastruloids have the potential to recapitulate the main ontogenetic events observed in intact embryos, including the internalization of mesodermal progenitors and eye development, as followed withZic:GFPreporter lines. In addition, intermorph cell grafts resulted in proper integration of exogenous cells into the embryonic tissues, with lineages becoming more restricted from mid-blastula to gastrula. The implementation of these approaches inA. mexicanuswill bring new light on the cascades of events, from the maternal pre-patterning of the early embryo to the evolution of brain regionalization.
Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure
Authors: Osman Noha , Shawky Abd-El-Monsif , Brylinski Michal 
Published: October 2020

AbstractNumerous genome-wide association studies (GWAS) conducted to date revealed genetic variants associated with various diseases, including breast and prostate cancers. Despite the availability of these large-scale data, relatively few variants have been functionally characterized, mainly because the majority of single-nucleotide polymorphisms (SNPs) map to the non-coding regions of the human genome. The functional characterization of these non-coding variants and the identification of their target genes remain challenging. In this communication, we explore the potential functional mechanisms of non-coding SNPs by integrating GWAS with the high-resolution chromosome conformation capture (Hi-C) data for breast and prostate cancers. We show that more genetic variants map to regulatory elements through the 3D genome structure than the 1D linear genome lacking physical chromatin interactions. Importantly, the association of enhancers, transcription factors, and their target genes with breast and prostate cancers tends to be higher when these regulatory elements are mapped to high-risk SNPs through spatial interactions compared to simply using a linear proximity. Finally, we demonstrate that topologically associating domains (TADs) carrying high-risk SNPs also contain gene regulatory elements whose association with cancer is generally higher than those belonging to control TADs containing no high-risk variants. Our results suggest that many SNPs may contribute to the cancer development by affecting the expression of certain tumor-related genes through long-range chromatin interactions with gene regulatory elements. Integrating large-scale genetic datasets with the 3D genome structure offers an attractive and unique approach to systematically investigate the functional mechanisms of genetic variants in disease risk and progression.
A global database of photosynthesis model parameters, and modelled photosynthetic responses from every major terrestrial plant clade
Authors: Rostamza Mina , McNickle Gordon G. 
Published: October 2020

ABSTRACTPlant photosynthesis is a major part of the global carbon cycle and climate system. Carbon capture by C3plants is most often modelled using the Farquhar-von-Caemmerer-Berry (FvCB) equations. We undertook a global synthesis of all parameters required to solve the FvCB model. The publicly available dataset we assembled includes 3663 observations from 336 different C3plant species among 96 taxonomic families coming from every major vascular plant clade (lycophytes, ferns, gymnosperms, magnoliids, eudicots and monocots). Geographically, the species in the database have distributions that span the majority of the globe. We used the model to predict photosynthetic rates for a hypothetical average plant in each major terrestrial plant clade and find that generally plants have dramatically increased their photosynthetic abilities through evolutionary time, with the average monocot (the youngest clade) achieving maximum rates of photosynthesis almost double that of the average lycophyte (the oldest clade). We also solved the model for different hypothetical average plant functional types (PFTs) and find that herbaceous species generally have much higher rates of photosynthesis compared to woody plants. Indeed, the maximum photosynthetic rate of graminoids is almost three times the rate of the average tree. The resulting functional responses to increasing CO2in average hypothetical PFTs would suggest that most groups are already at or near their maximum rate of photosynthesis. However, phylogenetic analysis showed that there was no evidence of niche conservatism with most variance occurring within, rather than among clades (K=0.357, p=0.001). This high within-group variability suggests that average PFTs may obscure important plant responses to increasing CO2. Indeed, when we solved the model for each of the 3663 individual observations, we found that, contrary to the predictions of hypothetical average PFTs, that most plants are predicted to be able to increase their photosynthetic rates. These results suggest that global models should seek to incorporate high within-group variability to accurately predict plant photosynthesis in response to a changing climate.
Evaluating state space discovery by persistent cohomology in the spatial representation system
Authors: Kang Louis , Xu Boyan , Morozov Dmitriy 
Published: October 2020

AbstractPersistent cohomology is a powerful technique for discovering topological structure in data. Strategies for its use in neuroscience are still undergoing development. We comprehensively and rigorously assess its performance in simulated neural recordings of the brain’s spatial representation system. Grid, head direction, and conjunctive cell populations each span low-dimensional topological structures embedded in high-dimensional neural activity space. We evaluate the ability for persistent cohomology to discover these structures for different dataset dimensions, variations in spatial tuning, and forms of noise. We quantify its ability to decode simulated animal trajectories contained within these topological structures. We also identify regimes under which mixtures of populations form product topologies that can be detected. Our results reveal how dataset parameters affect the success of topological discovery and suggest principles for applying persistent cohomology, as well as persistent homology, to experimental neural recordings.
Temporal transitions in post-mitotic neurons throughout theC. elegansnervous system
Authors: Sun HaoSheng , Hobert Oliver 
Published: October 2020

SUMMARYIn most animals, the majority of the nervous system is generated and assembled into neuronal circuits during embryonic development. However, during juvenile stages, nervous systems still undergo extensive anatomical and functional changes to eventually form a fully mature nervous system by the adult stage. The molecular changes in post-mitotic neurons across post-embryonic development and the genetic programs that control these temporal transitions are not well understood. Using the model organismC. elegans, we comprehensively characterized the distinct functional states (locomotor behavior) and corresponding distinct molecular states (transcriptome) of the post-mitotic nervous system across temporal transitions from early post-embryonic periods to adulthood. We observed pervasive changes in gene expression, many of which are controlled by the developmental upregulation of the conserved heterochronic miRNAlin-4/mir-125and the subsequent promotion of a mature neuronal transcriptional program through the repression of its target, the transcription factorlin-14. The functional relevance of these molecular transitions are exemplified by a temporally regulated target gene of thelin-14transcription factor,nlp-45, a neuropeptide-encoding gene. We found thatnlp-45is required for temporal transitions in exploratory activity across larval stages, across sexual maturation, and into a diapause arrest stage. Our studies provide new insights into regulatory strategies that control neuron-type specific gene batteries to modulate distinct behaviors states across temporal, sex and environmental dimensions of post-embryonic development, and also provides a rich atlas of post-embryonic molecular changes to uncover additional regulatory mechanisms.
Production of ORF8 protein from SARS-CoV-2 using an inducible virus-mediated expression system in suspension-cultured tobacco BY-2 cells
Authors: Imamura Tomohiro , Isozumi Noriyoshi , Higashimura Yasuki , Ohki Shinya , Mori Masashi 
Published: October 2020

AbstractCOVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which spread worldwide in 2020, is an urgent problem to be overcome. The ORF8 of SARS-CoV-2 has been suggested to be associated with the symptoms of COVID-19, according to reports of clinical studies. However, little is known about the function of ORF8. As one of the ways to advance the functional analysis of ORF8, mass production of ORF8 with the correct three-dimensional structure is necessary. In this study, we attempted to produce ORF8 protein by chemically inducible protein production system using tobacco BY-2 cells. An ORF8-producing line was generated by the Agrobacterium method. As a result, the production of ORF8 of 8.8 ± 1.4 mg/L of culture medium was confirmed. SDS-PAGE and nuclear magnetic resonance (NMR) analysis confirmed that the ORF8 produced by this system is a dimeric form with a single structure, unlike that produced in Escherichia coli. Furthermore, it was suggested that the ORF8 produced by this system was glycosylated. Through this study, we succeeded in producing ORF8 folded into a single structure in a chemically inducible protein production system using tobacco BY-2 cells. It is expected that the functional analysis of ORF8 will be advanced using the ORF8 produced by this system and that it will greatly contribute to the development of antibodies and therapeutic agents targeting ORF8.
Evolutionary history of the Galápagos Rail revealed by ancient mitogenomes and modern samples
Authors: Chaves Jaime A. , Martinez-Torres Pedro J. , Depino Emiliano A. , Espinoza-Ulloa Sebastian , García-Loor Jefferson , Beichman Annabel , Stervander Martin 
Published: October 2020

AbstractThe biotas of the Galápagos Islands are probably one of the best studied island systems and have provided a broad model of insular species’ origins and evolution. Nevertheless, some Galápagos species remain poorly characterized, such as the Galápagos RailLaterallus spilonota. This bird species is one of the less explored groups of endemic vertebrates on these islands, due to its elusive behavior, cryptic plumage and restricted distribution. To date there is no genetic assessment of its origins and sister relationships to other taxa, and importantly, there is no data on its current genetic diversity. This lack of information is critical given the adverse fate of island rail species around the world in the recent past. Here we examine the genetics of Galápagos Rails using a combination of mitogenomede novoassembly with multi-locus sequencing (mtDNA+nuDNA) from both modern and historical samples. We show that the Galápagos Rail is part of the ‘American black rail clade’, sister to Black RailL. jamaicensis, with a colonization of Galápagos dated to 1.2 Mya. The separate analysis of cytb, ND2, and RAG-1 markers demonstrates shallow population structure across sampled islands, possibly due to elevated island connectivity. Additionally, birds sampled from Pinta possessed the lowest levels of genetic diversity, most likely reflecting the impact of past bottlenecks due to habitat loss caused by invasive goats grazing on sensitive habitat. The data presented here highlights the low genetic diversity in this endemic rail species and suggests the use of genetic data (both modern and historical) to guide conservation efforts.
Polo-like kinase 1 independently controls microtubule-nucleating capacity and size of the centrosome
Authors: Ohta Midori , Zhao Zhiling , Wu Di , Wang Shaohe , Harrison Jennifer L. , Gómez-Cavazos J. Sebastián , Desai Arshad , Oegema Karen 
Published: October 2020

SUMMARYCentrosomes are composed of a centriolar core surrounded by a pericentriolar material (PCM) matrix that docks microtubule-nucleating γ-tubulin complexes. During mitotic entry, the PCM matrix increases in size and nucleating capacity in a process called centrosome maturation. Polo-like kinase 1 (PLK1) localizes to centrosomes and phosphorylates PCM matrix proteins to drive their self-assembly, which leads to PCM expansion; this expansion has been assumed to passively increase microtubule nucleation to support spindle assembly. Here, we show that PLK1 directly controls the generation of binding sites for γ-tubulin complexes on the PCM matrix, independently of PCM expansion. Selective inhibition of PLK1-dependent γ-tubulin docking leads to spindle defects and impaired chromosome segregation, without affecting PCM expansion, highlighting the importance of phospho-regulated centrosomal γ-tubulin docking sites in spindle assembly. Inhibiting both γ-tubulin docking and PCM expansion by mutating substrate target sites fully accounts for the actions of PLK-1 in transforming the centrosome during mitotic entry.Summary StatementPolo-like kinase 1-mediated physical expansion of centrosomes during mitotic entry is proposed to passively increase their microtubule nucleating capacity. Ohta et al. show instead that generation of microtubule-nucleating sites is directly controlled by Polo-like kinase 1, independently of centrosome size.