bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tomato roots sense horizontal/vertical mechanical impedance and divergently modulate root/shoot metabolome
Authors: Kumari Alka , Nongmaithem Sapana , Devulapalli Sameera , Sreelakshmi Yellamaraju , Sharma Rameshwar 
Published: February 2021

AbstractPlant roots encounter coarse environs right after emergence from the seeds. Little is known about metabolic changes enabling roots to overcome the soil impedance. Tomato seedlings grown vertically or horizontally, at increasing hardness, exhibited lateral roots proliferation, shorter hypocotyls, and primary roots. In primary root tips, hardness-elicited loss of amyloplasts staining; induced ROS and NO accumulation. The levels of IBA, zeatin, jasmonates, and salicylic acids markedly differed in roots and shoots exposed to increasing hardness. Hardness lowered IAA and elevated ABA levels, while increased ethylene emission was confined to horizontally-impeded seedlings. The trajectories of metabolomic shifts distinctly differed between vertically/horizontally-impeded roots/shoots. In horizontal roots, amino acids were the major affected group, while in vertical roots, sugars were the major group. Commonly affected metabolites in roots and shoots, trehalose, dopamine, caffeoylquinic acid, and suberic acid, hallmarked the signature for hardness. Increasing hardness loweredSnRK1aexpression in roots/shoots implying regulation of metabolic homeostasis by the SnRK1 signalling module. Our data suggest that though hardness is a common denominator, roots sense the horizontal/vertical orientation and correspondingly modulate metabolite profiles.Significance statementWe show that the tomato roots sense the magnitude of hardness as well as the horizontal and vertical orientation. The hardness divergently modulates the phytohormone and metabolite levels in roots and shoots. The trajectory of the metabolic shift in vertically-grown seedling distinctly differs from horizontally-grown seedlings. ABA and trehalose were the hallmark of hardness stress and may influence metabolic alteration via the SNRK signalling pathway.
The evolution of the metazoan Toll receptor family and its expression during protostome development
Authors: Orús-Alcalde Andrea , Lu Tsai-Ming , Hejnol Andreas 
Published: February 2021

AbstractBackgroundToll-like receptors (TLRs) play a crucial role in immunity and development. They contain leucine-rich repeat domains, one transmembrane domain, and one Toll/IL-1 receptor domain. TLRs have been classified into V-type/scc and P-type/mcc TLRs, based on differences in the leucine-rich repeat domain region. Although TLRs are widespread in animals, detailed phylogenetic studies of this gene family are lacking. Here we aim to uncover TLR evolution by conducting a survey and a phylogenetic analysis in species across Bilateria. To discriminate between their role in development and immunity we furthermore analyzed stage-specific transcriptomes of the ecdysozoansPriapulus caudatusandHypsibius exemplaris, and the spiraliansCrassostrea gigasandTerebratalia transversa.ResultsWe detected a low number of TLRs in ecdysozoan species, and multiple independent radiations within the Spiralia. V-type/scc and P-type/mcc type-receptors are present in cnidarians, protostomes and deuterostomes, and therefore they emerged early in TLR evolution, followed by a loss in xenacoelomorphs. Our phylogenetic analysis shows that TLRs cluster into three major clades: clade α is present in cnidarians, ecdysozoans, and spiralians; clade β in deuterostomes, ecdysozoans, and spiralians; and clade γ is only found in spiralians. Our stage-specific transcriptome andin situhybridization analyses show that TLRs are expressed during development in all species analyzed, which indicates a broad role of TLRs during animal development.ConclusionsOur findings suggest that the bilaterian TLRs likely emerged by duplication from a single TLR encoding gene (proto-TLR) present in the last common cnidarian-bilaterian ancestor. Thisproto-TLR gene duplicated before the split of protostomes and deuterostomes; a second duplication occurred in the lineage to the Trochozoa. While all three clades further radiated in several spiralian lineages, specific TLRs clades have been presumably lost in others. Furthermore, the expression of the majority of these genes during protostome ontogeny suggests their involvement in immunity and development.
Integrated spatial models foster complementarity between monitoring programs in producing large-scale bottlenose dolphin indicators
Authors: Lauret Valentin , Labach Hélène , Turek Daniel , Laran Sophie , Gimenez Olivier 
Published: February 2021

AbstractOver the last decades, large-scale ecological projects have emerged that require collecting ecological data over broad spatial and temporal coverage. Yet, obtaining relevant information about large-scale population dynamics from a single monitoring program is challenging, and often several sources of data, possibly heterogeneous, need to be integrated. In this context, integrated models combine multiple data types into a single analysis to quantify population dynamics of a targeted population. When working at large geographical scales, integrated spatial models have the potential to produce spatialised ecological estimates that would be difficult to obtain if data were analysed separately.In this paper, we illustrate how spatial integrated modelling offers a relevant framework for conducting ecological inference at large scales. Focusing on the Mediterranean bottlenose dolphins (Tursiops truncatus), we combined 21,464 km of photo-identification boat surveys collecting spatial capture-recapture data with 24,624 km of aerial line-transect following a distance-sampling protocol. We analysed spatial capture-recapture data together with distance-sampling data to estimate abundance and density of bottlenose dolphins. We compared the performances of the distance sampling model and the spatial capture-recapture model fitted independently, to our integrated spatial model.The outputs of our spatial integrated models inform bottlenose dolphin ecological status in the French Mediterranean Sea and provide ecological indicators that are required for regional scale ecological assessments like the EU Marine Strategy Framework Directive. We argue that integrated spatial models are widely applicable and relevant to conservation research and biodiversity assessment at large spatial scales.
Refining the Identity and Role of Kv4 Channels in Mouse Substantia Nigra Dopaminergic Neurons
Authors: Haddjeri-Hopkins Alexis , Tapia Mónica , Ramirez-Franco Jorge , Tell Fabien , Marqueze-Pouey Béatrice , Amalric Marianne , Goaillard Jean-Marc 
Published: February 2021

ABSTRACTSubstantia nigra pars compacta (SNc) dopaminergic (DA) neurons display a peculiar electrical phenotype characterized in vitro by a spontaneous tonic regular activity (pacemaking activity), a broad action potential and a biphasic post-inhibitory response. Several studies in rodents have underlined the central role played by the transient A-type current (IA) in the control of pacemaking activity and post-inhibitory rebound properties, thereby influencing both DA release and the physiological response of SNc neurons to incoming inhibitory inputs. Kv4.3 potassium channels were considered to be fully responsible for IA in these neurons, their density being tightly related to pacemaking frequency. In spite of this crucial electrophysiological role, we show that Kv4.3-/- transgenic mice exhibit minor alterations in locomotion and motor learning, although no compensation by functionally overlapping ion channels is observed in Kv4.3-/- SNc DA neurons. Using antigen retrieval immunohistochemistry, we further demonstrate that Kv4.2 potassium channels are also expressed in SNc DA neurons, even though their contribution to IA appears significant only in a minority of neurons (~5-10%). Using correlative analysis on recorded electrophysiological parameters and multi-compartment modeling, we then demonstrate that, rather than its conductance level, IA gating kinetics (inactivation time constant) appear as the main biophysical property defining post-inhibitory rebound delay and pacemaking frequency. Moreover, we show that the hyperpolarization-activated current (IH) has an opposing and complementary influence on the same firing features, and that the biophysical properties of IA and IH are likely coregulated in mouse SNc DA neurons.SIGNIFICANCE STATEMENTSubstantia nigra pars compacta (SNc) dopaminergic (DA) neurons are characterized by pacemaking activity, a broad action potential and biphasic post-inhibitory response. The A-type transient potassium current (IA) plays a central role in both pacemaking activity and post-inhibitory response. While it was thought so far that Kv4.3 ion channels were fully responsible for IA, using a Kv4.3-/- transgenic mouse and antigen retrieval immunohistochemistry we demonstrate that Kv4.2 channels are also expressed in SNc DA neurons, although their contribution is significant in a minority of neurons only. Using electrophysiological recordings and computational modeling, we then demonstrate that IA gating kinetics and its functional complementarity with the hyperpolarization-activated current are major determinants of both pacemaking activity and post-inhibitory response in SNc DA neurons.
Early, color-specific neural responses to object color knowledge
Authors: Retter Talia L. , Gao Yi , Jiang Fang , Rossion Bruno , Webster Michael A. 
Published: February 2021

AbstractSome familiar objects are associated with specific colors, e.g., rubber ducks with yellow. Whether and at what stage neural responses occur to these color associations remain open questions. We tested for frequency-tagged electroencephalogram (EEG) responses to periodic presentations of yellow-associated objects, shown among sequences of non-periodic blue-, red-, and green-associated objects. Both color and grayscale versions of the objects elicited yellow-specific responses, indicating an automatic activation of color knowledge from object shape. Follow-up experiments replicated these effects with green-specific responses, and demonstrated modulated responses for incongruent color-object associations. Importantly, the onset of color-specific responses was as early to grayscale as actually colored stimuli (before 100 ms), the latter additionally eliciting a conventional later response (approximately 140-230 ms) to actual stimulus color. This suggests that the neural representation of familiar objects includes both diagnostic shape and color properties, such that shape can elicit associated color-specific responses before actual color-specific responses occur.
Molecular basis for two stereoselective Diels-Alderases that produce decalin skeletons
Authors: Fujiyama Keisuke , Kato Naoki , Re Suyong , Kinugasa Kiyomi , Watanabe Kohei , Takita Ryo , Nogawa Toshihiko , Hino Tomoya , Osada Hiroyuki , Sugita Yuji , Takahashi Shunji , Nagano Shingo 
Published: February 2021

SummaryMolecular chirality, discovered by Louis Pasteur in the middle of the 19th century1, is found in most primary and secondary metabolites. Particularly, the so-called natural products are rich in chiral centres2. The stereochemistry of natural products is strictly recognized in living organisms, and is thus closely related to their biological functions. The Diels–Alder (DA) reaction, which forms a six-membered ring with up to four chiral centres, is a fundamental practical reaction for C–C bond formation in synthetic chemistry3. Nature has also adopted this reaction to elaborate the complex structures of natural products using enzymes derived from various progenitor proteins4-7. Although enzymes catalysing the DA reaction, Diels–Alderases (DAases), have attracted increasing attention, little is known about the molecular mechanism by which they control the stereochemistry and perform catalysis. Here, we solved the X-ray crystal structures of a pair of decalin synthases, Fsa2 and Phm7, that catalyse intramolecular DA reactions to form enantiomeric decalin scaffolds during biosynthesis of the HIV-1 integrase inhibitor equisetin and its stereochemical opposite, phomasetin8,9. Based on the crystal structures, docking simulations followed by all-atom molecular dynamics simulations provided dynamic binding models demonstrating the folding of linear polyenoyl tetramic acid substrates in the binding pocket of these enzymes, explaining the stereoselectivity in the construction of decalin scaffolds. Site-directed mutagenesis studies verified the binding models and, in combination with density functional theory calculations, clarified how hydrophilic amino acid residues in the Phm7 pocket regulate and catalyse the stereoselective DA reaction. This study highlights the distinct molecular mechanisms of the enzymatic DA reaction and its stereoselectivity experimentally and computationally. We anticipate that clarified molecular mechanism herein provides not only the basic understanding how these important enzymes work but also the guiding principle to create artificial enzymes that produce designer bioactive molecules.
Structural analysis of viral ExoN domains reveals polyphyletic hijacking events
Authors: Cruz-González A. , Muñoz-Velasco I. , Cottom-Salas W. , Becerra A. , Campillo-Balderas J.A. , Hernández-Morales R. , Vázquez-Salazar A. , Jácome R. , Lazcano A. 
Published: February 2021

AbstractNidoviruses and arenaviruses are the only known RNA viruses encoding a 3’-5’ exonuclease domain (ExoN). The proofreading activity of the ExoN domain has played a key role in the growth of nidoviral genomes, while in arenaviruses this domain partakes in the suppression of the host innate immune signaling. Sequence and structural homology analyses suggest that these proteins have been hijacked from cellular hosts many times. Analysis of the available nidoviral ExoN sequences reveals a high conservation level comparable to that of the viral RNA-dependent RNA polymerases (RdRp), which are the most conserved viral proteins. Two highly preserved zinc fingers are present in all nidoviral exonucleases, while in the arenaviral protein only one zinc finger can be identified. This is in sharp contrast with the reported lack of zinc fingers in cellular ExoNs, and opens the possibility of therapeutic strategies in the struggle against COVID-19.
Genome-scale metabolic modelling ofP. thermoglucosidasiusNCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism
Authors: Mol Viviënne , Bennett Martyn , Sánchez Benjamín J. , Lisowska Beata K. , Herrgård Markus J. , Nielsen Alex Toftgaard , Leak David J. , Sonnenschein Nikolaus 
Published: February 2021

AbstractParageobacillus thermoglucosidasiusrepresents a thermophilic, facultative anaerobic bacterial chassis, with several desirable traits for metabolic engineering and industrial production. To further optimize strain productivity, a systems level understanding of its metabolism is needed, which can be facilitated by a genome-scale metabolic model. Here, we presentp-thermo, the most complete, curated and validated genome-scale model (to date) ofParageobacillus thermoglucosidasiusNCIMB 11955. It spans a total of 890 metabolites, 1175 reactions and 917 metabolic genes, forming an extensive knowledge base forP. thermoglucosidasiusNCIMB 11955 metabolism. The model accurately predicts aerobic utilization of 22 carbon sources, and the predictive quality of internal fluxes was validated with previously published13C-fluxomics data. In an application case,p-thermowas used to facilitate more in-depth analysis of reported metabolic engineering efforts, giving additional insight into fermentative metabolism. Finally,p-thermowas used to resolve a previously uncharacterised bottleneck in anaerobic metabolism, by identifying the minimal required supplemented nutrients (thiamin, biotin and iron(III)) needed to sustain anaerobic growth. This highlights the usefulness ofp-thermofor guiding the generation of experimental hypotheses and for facilitating data-driven metabolic engineering, expanding the use ofP. thermoglucosidasiusas a high yield production platform.
Single-component optogenetic tools for inducible RhoA GTPase signaling
Authors: Berlew Erin E. , Kuznetsov Ivan A. , Yamada Keisuke , Bugaj Lukasz J. , Boerckel Joel D. , Chow Brian Y. 
Published: February 2021

ABSTRACTWe created optogenetic tools to control RhoA GTPase, a central regulator of actin organization and actomyosin contractility. RhoA GTPase, or its upstream activating GEF effectors, were fused to BcLOV4, a photoreceptor that can be dynamically recruited to the plasma membrane by a light-regulated protein-lipid electrostatic interaction with the inner leaflet. Direct membrane recruitment of these effectors induced potent contractile signaling sufficient to separate adherens junctions in response to as little as one pulse of blue light. Cytoskeletal morphology changes were dependent on the alignment of the spatially patterned stimulation with the underlying cell polarization. RhoA-mediated cytoskeletal activation induced YAP nuclear localization within minutes and subsequent mechanotransduction, verified by YAP- TEAD transcriptional activity. These single-component tools, which do not require protein binding partners, offer spatiotemporally precise control over RhoA signaling that will advance the study of its diverse regulatory roles in cell migration, morphogenesis, and cell cycle maintenance.
Mouse oocytes do not contain a Balbiani body
Authors: Dhandapani Laasya , Salzer Marion C. , Duran Juan M. , Zaffagnini Gabriele , De Guirior Cristian , Martínez-Zamora Maria Angeles , Böke Elvan 
Published: February 2021

ABSTRACTOocytes spend the majority of their lifetime in a primordial, dormant state. Unlike many somatic cell types and mature oocytes, the cellular and molecular biology of primordial oocytes is largely unexplored. Yet, studying their cellular biology is necessary to understand the mechanisms through which oocytes maintain cellular fitness for decades, and why they eventually fail with age.A hallmark of primordial oocytes in many species is the Balbiani body, a non-membrane bound compartment that contains the majority of mitochondria in the oocyte cytoplasm. The Balbiani body has been proposed to be essential for maintaining mitochondria in a healthy state during long-lasting dormancy, however, the architecture and function of the mammalian Balbiani body remains unknown.Here, we develop enabling methods for live-imaging based comparative characterization ofXenopus, mouse and human primordial oocytes. We show that primordial oocytes in all three vertebrate species contain active mitochondria, Golgi apparatus and lysosomes. We further demonstrate that human andXenopusoocytes have a Balbiani body characterized by a dense accumulation of mitochondria in their cytoplasm. However, despite previous reports, we did not find a Balbiani body in mouse oocytes. Instead, we demonstrate what was previously used as a marker for the Balbiani body in mouse primordial oocytes is in fact a ring-shaped Golgi apparatus that is not functionally associated with oocyte dormancy. Our work provides the first insights into the organisation of the cytoplasm in mammalian primordial oocytes, and clarifies relative advantages and limitations of choosing different model organisms for studying oocyte dormancy.
MESOMELIC DYSPLASIAS ASSOCIATED WITH THEHOXDLOCUS ARE CAUSED BY REGULATORY REALLOCATIONS
Authors: Bolt Christopher Chase , Lopez-Delisle Lucille , Mascrez Bénédicte , Duboule Denis 
Published: February 2021

ABSTRACTSome human families display severe shortening and bending of the radius and ulna, a condition referred to as mesomelic dysplasia. Many of these families contain chromosomal rearrangements at 2q31, where the humanHOXDlocus maps. In mice, the dominant X-ray-inducedUlnalessinversion of theHoxDgene cluster produces a similar phenotype suggesting that the same mechanism is responsible for this pathology in humans and mice. Amongst the proposed explanations, the various alterations to the genomic structure ofHOXDcould exposeHoxd13to proximal limb enhancers, leading to its deleterious gain-of-expression in the embryonic forelimb. To assess this hypothesis, we used an engineered 1Mb large inversion including theHoxDgene cluster, in order to positionHoxd13within a chromatin domain rich in proximal limb enhancers. We show that these enhancers contact and activateHoxd13in proximal cells, concomitant to the formation of a mesomelic dysplasia phenotype. A secondary mutation in the coding frame of the HOXD13 protein in-ciswith the inversion completely rescued the limb alterations, demonstrating that ectopic HOXD13 is indeed the unique cause of this bone anomaly. Single cell expression analysis and evaluation of HOXD13 binding sites in cells from this ectopic expression domain suggests that the phenotype arises primarily by acting through genes normally controlled by HOXD13 in distal limb cells. Altogether, these results provide a conceptual and mechanistic framework to understand and unify the molecular origins of human mesomelic dysplasia associated with 2q31.
Premium versus affordable clothing retailers: what are customer expectations for satisfaction and repurchase intentions?
Authors: Cunningham Nicole , De Meyer-Heydenrych Christine 
Published: February 2021

PurposeWithin the highly competitive clothing retail industry, retailers (both affordable and premium) need to consider which customer experience elements drive customer satisfaction and repurchase intentions. The purpose of this study is to determine whether customer expectations are different for various types of clothing retailers, and what customers specifically expect when purchasing from a retailer.Design/methodology/approachFor this study, a positivistic quantitative research design and a non-probability convenience sampling method were used. A total of 222 useable questionnaires were used to conduct descriptive statistics. Confirmatory factor analysis, structural equation modelling and multi-group analysis were run to test the hypotheses.FindingsThe results indicate that customers expect affordable retailers to provide them with convenience and to create a positive shopping experience, while premium clothing retailers should offer added-value and convenience. In addition, the presence of other customers influences the experience. For both groups, satisfaction was a predictor of loyalty, which, in turn, was a predictor of repurchase intentions.Originality/valueThe study is unique as it compares the customer expectations for satisfaction and repurchase intentions for both affordable retailers and premium retailers. The study is conducted in an emerging market context where the growth of the retailing industry is visible. By conducting this study, both affordable and premium clothing retailers are more informed with regards to their customer's expectations and how those expectations should be managed in order to ensure satisfaction and repurchase intention.