bluuebunny/crossref_metadata_2025_split huggingface dataset:
The non-redundant nature of the Axin2 regulatory network in the canonical Wnt signaling pathway
Authors: Moshkovsky Ana R , Kirschner Marc W 
Published: April 2021

Axin is one of two essential scaffolds in the canonical Wnt pathway that converts signals at the plasma membrane to signals inhibiting the degradation of β-catenin, leading to its accumulation and specific gene activation. In vertebrates there are two forms of Axin, Axin1 and Axin2, which are similar at the protein level and genetically redundant. We show here that differential regulation of the two genes on the transcriptional and proteostatic level confers robustness and differential responsiveness that can be used in tissue specific regulation. Such subtle features may distinguish other redundant gene pairs that are commonly found in vertebrates through gene knockout experiments.Significance StatementThe mystery of two functionally redundant Axin genes in all vertebrates are can now be explained by the demonstration that they form a nested proteostatic and transcriptional feedback system that confers regulatory options in different developmental settings, a form of dynamic versatility that may explain the widespread occurrence of closely related seemingly redundant genes with similar functions.
Fast Bayesian inference of phylogenies from multiple continuous characters
Authors: Zhang Rong , Drummond Alexei J. , Mendes Fábio K. 
Published: April 2021

AbstractTime-scaled phylogenetic trees are an ultimate goal of evolutionary biology and a necessary ingredient in comparative studies. The accumulation of genomic data has resolved the tree of life to a great extent, yet timing evolutionary events remains challenging if not impossible without external information such as fossil ages and morphological characters. Methods for incorporating morphology in tree estimation have lagged behind their molecular counter-parts, especially in the case of continuous characters. Despite recent advances, such tools are still direly needed as we approach the limits of what molecules can teach us. Here, we implement a suite of state-of-the-art methods for leveraging continuous morphology in phylogenetics, and by conducting extensive simulation studies we thoroughly validate and explore our methods’ properties. While retaining model generality and scalability, we make it possible to estimate absolute and relative divergence times from multiple continuous characters while accounting for uncertainty. We compile and analyze one of the most data-type diverse data sets to date, comprised of contemporaneous and ancient molecular sequences, and discrete and continuous characters from living and extinct Carnivora taxa. We conclude by synthesizing lessons about our method’s behavior, and suggest future research venues.
Segment number threshold determines juvenile onset of germline cluster proliferation inPlatynereis dumerilii
Authors: Kuehn Emily , Clausen David S. , Null Ryan W. , Metzger Bria M. , Willis Amy D. , Özpolat B. Duygu 
Published: April 2021

AbstractMany animals rely on sexual reproduction to propagate by using gametes (oocytes and sperm). Development of sexual characters and generation of gametes are tightly coupled with the growth of an organism.Platynereis dumeriliiis a marine segmented worm which has been used to study germline development and gametogenesis.Platynereishas 4 Primordial Germ Cells (PGCs) that arise early in development and these cells are thought to give rise to germ cell clusters found across the body in the juvenile worms. The germ cell clusters eventually form the gametes. The stages of germline development and how the 4 PGCs become the numerous germ cell clusters are not well-documented in the juvenile stages.Platynereis, like other segmented worms, grows by adding new segments at its posterior end. The number of segments generally reflect the growth state of the worms and therefore is a useful and easily measurable growth state metric. To understand how growth correlates with development and gametogenesis, we investigated germline development across several developmental stages using germline/multipotency markers. We found that segment number predicted the state of germline development and the abundance of germline clusters. Additionally, we found that keeping worms short in segment number via changing external conditions or via amputations supported segment number threshold requirement for germline development. Finally, we asked if these clusters inPlatynereisplay a role in regeneration (as similar free-roaming cells are observed inHydraand planarian regeneration) and found that the clusters were not required for regeneration inPlatynereis, suggesting a strictly germline nature. Overall, these molecular analyses suggest a previously unidentified developmental transition dependent on the growth state in juvenilePlatynereiswhen germline proliferation is substantially increased.
Redox sensitive E2 Rad6 controls cellular response to oxidative stress via K63 ubiquitination of ribosomes
Authors: Simões Vanessa , Harley Lana , Cizubu Blanche K. , Zhou Ye , Pajak Joshua , Snyder Nathan A. , Bouvette Jonathan , Borgnia Mario J. , Arya Gaurav , Bartesaghi Alberto , Silva Gustavo M. 
Published: April 2021

AbstractProtein ubiquitination is an essential process that rapidly regulates protein synthesis, function, and fate in dynamic environments. Among its non-proteolytic functions, K63 ubiquitin accumulates in yeast cells exposed to oxidative stress, stalling ribosomes at elongation. K63 ubiquitin conjugates accumulate because of redox inhibition of the deubiquitinating enzyme Ubp2, however, the role and regulation of ubiquitin conjugating enzymes in this pathway remained unclear. Here we found that the E2 Rad6 binds and modifies elongating ribosomes during oxidative stress. We elucidated a mechanism by which Rad6 and its human homolog UBE2A are redox-regulated by forming reversible disulfides with the E1 activating enzyme, Uba1. We further showed that Rad6 activity is necessary to regulate translation, antioxidant defense, and adaptation to stress. Finally, we showed that Rad6 is required to induce phosphorylation of the translation initiation factor eIF2α, providing a novel link for K63 ubiquitin, elongation stalling, and the integrated stress response.
Structures of active melanocortin-4 receptor−Gs-protein complexes with NDP-α-MSH and setmelanotide
Authors: Heyder Nicolas A. , Kleinau Gunnar , Speck David , Schmidt Andrea , Paisdzior Sarah , Szczepek Michal , Bauer Brian , Koch Anja , Gallandi Monique , Kwiatkowski Dennis , Bürger Jörg , Mielke Thorsten , Beck-Sickinger Annette , Hildebrand Peter W. , Spahn Christian M. T. , Hilger Daniel , Schacherl Magdalena , Biebermann Heike , Hilal Tarek , Kühnen Peter , Kobilka Brian K. , Scheerer Patrick 
Published: April 2021

SUMMARYThe melanocortin-4 receptor (MC4R), a hypothalamic master regulator of energy homeostasis and appetite, is a G-protein coupled receptor and a prime target for the treatment of obesity. Here, we present cryo-electron microscopy structures of MC4R− Gs-protein complexes with two recently FDA-approved drugs, the peptide agonists NDP-α-MSH and setmelanotide, with 2.9 Å and 2.6 Å resolution. Together with signaling data, the complex structures reveal the agonist-induced origin of transmembrane helix (TM) 6 regulated receptor activation. In both structures, different ligand binding modes of NDP-α-MSH, a high-affinity variant of the endogenous agonist, and setmelanotide, an anti-obesity drug with biased signaling, underline the key role of TM3 for ligand-specific interactions and of calcium ion as a ligand-adaptable cofactor. The agonist-TM3 interplay subsequently impacts the receptor− Gs-protein interfaces, mainly at intracellular loop 2. These structures reveal mechanistic details of MC4R activation or inhibition and provide important insights into receptor selectivity that will facilitate the development of tailored anti-obesity drugs.
3D Flexible Refinement: Structure and Motion of Flexible Proteins from Cryo-EM
Authors: Punjani Ali , Fleet David J. 
Published: April 2021

AbstractSingle particle cryo-EM excels in determining static structures of biological macromolecules such as proteins. However, many proteins are dynamic, with their motion inherently linked to their function. Recovering the continuous motion and detailed 3D structure of flexible proteins from cryo-EM data has remained an open challenge. We introduce3D Flexible Refinement(3DFlex), a motion-based deep neural network model of continuous heterogeneity. 3DFlex directly exploits the knowledge that conformational variability of a protein is often the result of physical processes that transport density over space and tend to conserve mass and preserve local geometry. From 2D image data, the 3DFlex model jointly learns a single canonical 3D map, latent coordinate vectors that specify positions on the protein’s conformational landscape, and a flow generator that, given a latent position as input, outputs a 3D deformation field. This deformation field convects the canonical map into appropriate conformations to explain experimental images. Applied to experimental data, 3DFlex learns non-rigid motion spanning several orders of magnitude while preserving high-resolution details of secondary structure elements. Further, 3DFlex resolves canonical maps that are improved relative to conventional refinement methods because particle images contribute to the maps coherently regardless of the conformation of the protein in the image. Together, the ability to obtain insight into motion in macromolecules, as well as the ability to resolve features that are usually lost in cryo-EM of flexible specimens, will provide new insight and allow new avenues of investigation into biomolecular structure and function.
Citrullination of a phage displayed human peptidome library reveals the fine specificities of rheumatoid arthritis-associated autoantibodies
Authors: Román-Meléndez Gabriel D. , Monaco Daniel R. , Montagne Janelle M. , Quizon Rachel S. , Konig Maximilian F. , Astatke Mekbib , Darrah Erika , Larman H. Benjamin 
Published: April 2021

AbstractPost-translational modifications (PTMs) on proteins can be targeted by antibodies associated with autoimmunity. Despite a growing appreciation for their intrinsic role in disease, there is a lack of highly multiplexed serological assays to characterize the fine specificities of PTM-directed autoantibodies. In this study, we used the programmable phage display technology, Phage ImmunoPrecipitation Sequencing (PhIP-Seq), to profile rheumatoid arthritis (RA) associated anti-citrullinated protein antibody (ACPA) reactivities. Using both an unmodified and peptidylarginine deiminases (PAD)-modified phage display library consisting of ~250,000 overlapping 90 amino acid peptide tiles spanning the human proteome, PTM PhIP-Seq robustly identifies antibodies to citrulline-dependent epitopes. PTM PhIP-Seq was used to quantify key differences among RA patients, including PAD isoform specific ACPA profiles, and thus represents a powerful tool for proteome-scale antibody-binding analyses.
Identification of oxalyl-CoA synthetase gene (LsAAE3) and its regulatory role in β-ODAP biosynthesis in grasspea (Lathyrus sativusL.)
Authors: Kushwah Neetu Singh , Shanmugavadivel P.S. , Das Alok , Rathore Meenal , Singh Archana , Singh Narendra Pratap 
Published: April 2021

AbstractGrasspea is a popular pulse crop due to its hardiness and low cost of production. Presence of anti-nutritive factor ‘β-ODAP’ in its seeds and other plant parts hinder its widespread cultivation and usage. Oxalyl-CoA synthetase is one of the key enzyme of β-ODAP biosynthesis pathway, catalyses the conversion of oxalate to oxalyl-CoA.ACYL ACTIVATING ENZYME 3(AAE3) gene has been characterised to encode an oxalyl-CoA synthetase enzyme in many plant species. We report here the isolation of full lengthAAE3homolog in grasspea with a combination of PCR based strategy andin silicoanalysis. We first identifiedAAE3homolog by PCR using degenerate primers. The partial LsAAE3sequence showed 88% amino acids sequence identity with the characterisedAAE3gene ofM. truncatula. We then predicted the full lengthAAE3sequence using the publically available transcriptome datasets of grasspea. Determination ofLsAAE3gene and protein structure and phylogenetic relationship analysis strongly suggested thatLsAAE3is a true homolog ofAAE3gene. Expression profiling ofLsAAE3in grasspea varieties with contrast in β-ODAP content revealed its inverse relationship with the β-ODAP content,LsAAE3thus negatively regulates the synthesis of β-ODAP. Involvement of AAE3 encoded oxalyl-CoA synthetase in a CoA-dependent pathway of oxalate degradation is well proven in many plant species. We also identified the CoA-dependent pathway of oxalate degradation in grasspea. Based on these observations, we hypothesized thatLsAAE3may regulate β-ODAP content, possibly, by CoA-dependent pathway of oxalate degradation in grasspea. If this hypothesis is substantiated, genetic manipulation ofLsAAE3presents viable option for reducing β-ODAP content in grass pea.
Interferon‐α activates interleukin‐1 receptor‐associated kinase 1 to induce regulatory T‐cell apoptosis in patients with systemic lupus erythematosus
Authors: Li Mingfang , Yu Datang , Wang Yu , Luo Na , Han Guangming , Yang Bin 
Published: April 2021

AbstractImpaired regulatory T‐cell (Treg) responses and upregulated interleukin‐1 receptor‐associated kinase 1 (IRAK1) expression are associated with the development of human systemic lupus erythematosus (SLE). Here, we show that the levels of upregulated IRAK1 expression in circulating Tregs are correlated with the percentages of apoptotic Tregs, Systemic Lupus Erythematosus Disease Activity Index scores, and serum complement C3 levels in SLE patients. High levels of plasma interferon (IFN)‐α in SLE patients induced IRAK1 phosphorylation to trigger Treg apoptosis, which was mitigated by IRAK1 inhibitor (IRAK‐Inh) treatment. Bioinformatics indicated that IRAK1 activation was related to the IFN‐α/β and mitogen‐activated protein kinase (MAPK) signaling in Tregs and IFN‐α treatment induced the p38 and MAPK/ERK kinase 3/6 phosphorylation, which was attenuated by IRAK‐Inh in Tregs. Treatment with IRAK‐Inh effectively alleviated renal injury and promoted the survival of lupus‐prone B6.MRL‐Faslpr/Nju mice. Therefore, IFN‐α induced IRAK1 activation to promote Treg apoptosis, contributing to the pathogenesis of SLE and IFN‐α/IRAK1 may be therapeutic targets for SLE.
How vigilance shapes the functional response of herbivores
Authors: Sirot Etienne , Blanchard Pierrick , Loison Anne , Pays Olivier 
Published: April 2021

Abstract

Herbivores in quest of food have to attend areas where predators also concentrate their attacks. They have to deal with two conflicting demands, the need of feeding and that of avoiding predation. Using a theoretical approach, we study the influence of these antagonistic constraints on the shaping of an herbivore's foraging strategy and their consequences in terms of functional response.

In our model, the animal may curtail predation risk by being vigilant while foraging and by limiting its time of presence in the feeding area. Being vigilant means either stopping all feeding activities to scan for predators (exclusive vigilance) or using the time spent handling resources to do so, with reduced detection capacities (routine vigilance). Using an optimization criterium, we thus determine how long the animal will stay in the feeding area and how it will share its time and attention while present there, as a function of resource density and predation risk.

All behavioural variables show smooth but sometimes non‐monotonic variations in response to changes in these environmental conditions. When these variations are taken into account, the instantaneous intake rate of the herbivore, as well as the total biomass of plant consumed, increase in a decelerating but continuous manner with the patch's richness, in qualitative agreement with a type II functional response. This smooth pattern is explained by the possibility for the herbivore, when food abundance rises, to progressively redirect its attention to routine antipredator vigilance.

The relative importance of routine vigilance with respect to exclusive vigilance declines when predation risk increases, as well as the duration of the patch's visit and the total quantity of food eaten. The exact shape of the functional response is thus mediated by subtle adjustments of behavioural and attentional priorities, in response to variations in both food availability and predation risk.

A free Plain Language Summary can be found within the Supporting Information of this article.
Phenotypes of Pinus sylvestris are more coordinated under local harsher conditions across Europe
Authors: Benavides Raquel , Carvalho Bárbara , Matesanz Silvia , Bastias Cristina C. , Cavers Stephen , Escudero Adrián , Fonti Patrick , Martínez‐Sancho Elisabet , Valladares Fernando 
Published: April 2021

Abstract

Plant species that grow across environmental gradients show a range of trait expression, but traits do not vary independently. In fact, phenotypes are integrated expressions of multiple traits that covary due to trade‐offs among functions and processes. Understanding trait covariation structures will ultimately help with predicting species' responses to change and developing management actions.

We measured variation and covariation (a proxy of phenotypic integration) among functional traits of Pinus sylvestris from paired populations across its European distribution. Populations within a pair were close enough to be in gene flow contact but located in contrasting environmental conditions across a local gradient. Measured traits represented three axes of variation (groups of traits) related to a tree's competitive ability and the trade‐off between resource acquisition and conservation, namely plant size measures and stem and foliar traits.

Results revealed important intra‐ and inter‐population trait variability. In particular, at the population level, trait means shifted across the climatic gradient mainly described by mean annual temperature. Moreover, we found a higher degree of trait covariation in populations under harsher environments (i.e. lower environmental suitability for the species). This pattern was consistent within population pairs, suggesting that higher trait covariation may be adaptive, being more coordinated in sites with harsher conditions. At larger spatial scales, we found a less conclusive pattern with a trend of increasing covariation at the northern edge of the species distribution. This result suggests that at larger scales different processes may be involved in the trade‐off between the adaptive value of phenotypic covariation versus its constraints on trait combinations that may limit plant's response capability.

Synthesis. Trait covariation varies at different spatial scales, increasing under harsher conditions, and the robustness and repeatability of this pattern suggests its adaptive role for the species' responses to different environments.
Benefits to utilising ultrasound in examining the eye
Authors: Manton Joanna , Henry Caoimhe 
Published: April 2021

AbstractOcular ultrasound (US) is not one of ACEMs ‘big 5’ in terms of US capability that is expected of a trainee or FACEM. Most texts have a small chapter dedicated to ocular US but it is usually at the back or a subsection of a chapter where it is rarely seen or appreciated. However, it is a straightforward scan to perform with many benefits which will be discussed in this article. The eye offers an excellent medium for US beam penetration, making good quality images of the retina easy and quick to acquire. This has the added benefit of being able to share images with an ophthalmologist remotely, improving time to definitive treatment. It can also be used in patients who cannot cooperate with sitting at a slitlamp, for example moribund or trauma patients. The authors propose that ocular US teaching should be incorporated into the ACEM syllabus, being a vital adjunct to a comprehensive eye examination.
Continuous plasma exchange with dialysis for thrombotic microangiopathy in intensive care unit: Retrospective observational study
Authors: Satoh Kasumi , Okuyama Manabu , Irie Yasuhito , Kameyama Koumei , Kitamura Toshiharu , Nakae Hajime 
Published: April 2021

AbstractContinuous plasma exchange with dialysis is a novel method of blood purification and is a modification of the plasma exchange. Technically, this process suggests a reduction in adverse events, cost‐effectiveness, and compatibility with hemodynamic instability. The therapeutic effect of plasma exchange on thrombotic microangiopathies has been established. We present three clinical cases in the intensive care unit that illustrate continuous plasma exchange with dialysis as a flexible blood purification therapy for critically ill patients; a radical treatment, thrombotic microangiopathies; supportive therapy, multiple organ failure; and fluid balance regulator. The retrospective analysis of 13 continuous plasma exchange with dialysis sessions showed that the platelet count increased significantly (p = 0.0096) after its administration. The total protein, albumin, fibrinogen, or calcium did not decrease significantly after continuous plasma exchange with dialysis, suggesting therapeutic efficacy and fewer adverse events. A prospective study on thrombotic microangiopathies for continuous plasma exchange with dialysis is currently underway.
Effect of high‐pressure treatment and storage temperature on top‐quality (Montanera) Iberian dry‐cured pork sausages (chorizo)
Authors: Trejo A. , Martín M.J. , Gómez‐Quintana A. , Cava R. , García‐Parra J.J. , Ramírez M.R. 
Published: April 2021

AbstractThe stability after hydrostatic high pressure (HHP) (600 MPa/8 min/10 °C) and 180 days of storage at 4 and 20 °C was evaluated on Iberian dry‐cured pork sausages (chorizo) packaged sliced or as half‐pieces from pigs raised outdoors. Microbiological, physical–chemical, oxidative, and sensory changes were analyzed. The evolution of mesophilic aerobic and molds and yeasts counts was different in the half and sliced packaged pork sausages after processing and during storage. Sliced and half‐packaged pork sausages had instrumental color stability after HHP and during storage. TBA‐RS values were quite stable in both products. Protein oxidation values of pork sausage in half‐products were increased by at 20 °C. In sliced pork sausage, both HPP and 20 °C storage favored the development of protein oxidation at the end of storage. In the sensory analysis, the sliced product developed more rancidity than the half‐pieces during the storage. Therefore, the storage temperature has great importance for the preservation of dry‐cured pork sausages, the increases of protein oxidation, and rancidity could reduce the shelf‐life at these conditions. The presentation of the product is also relevant when HHP is applied, and this would also compromise the stability of the product when it is stored at room temperature.Practical ApplicationChorizo is a traditional dry‐fermented pork sausage that is generally considered to be microbiologically safe. However, the initial contamination of the raw materials, and some processes, such as the slicing or packaging, can compromise the safety of these products. Additionally, packaged dry‐cured sausages require long shelf‐life, and although they are normally stored at refrigeration temperature; sometimes, they are preserved at room temperature. The application of hydrostatic high pressure could increase the safety of dry‐cured meat products even when they are stored at room temperature. Initial characteristics of each type of pork sausage could determine their technological behavior during processing or during storage under different conditions.