bluuebunny/crossref_metadata_2025_split huggingface dataset:
Calcium-permeable cation channels are involved in uranium uptake in Arabidopsis thaliana
Authors: Sarthou Manon C.M. , Devime Fabienne , Baggio Célia , Figuet Sylvie , Alban Claude , Bourguignon Jacques , Ravanel Stéphane 
Published: June 2021

AbstractUranium (U) is a non-essential and toxic element that is taken up by plants from the environment. The assimilation pathway of U is still unknown in plants and any other organism. In this study, we provide several evidences that U is taken up by the roots of Arabidopsis thaliana through Ca2+-permeable cation channels. First, we showed that deprivation of Arabidopsis plants with calcium induced a 1.5-fold increase in the capacity of roots to accumulate U, suggesting that calcium deficiency promoted the radionuclide import pathway. Second, we showed that external calcium inhibits U accumulation in roots, suggesting a common route for the uptake of both cations. Third, we found that gadolinium, nifedipine and verapamil inhibit the absorption of U, suggesting that different types of Ca2+-permeable channels serve as a route for U uptake. Last, we showed that U bioaccumulation in Arabidopsis mutants deficient for the Ca2+-permeable channels MCA1 and ANN1 was decreased by 40%. This suggests that MCA1 and ANN1 contribute to the absorption of U in different zones and cell layers of the root. Together, our results describe for the first time the involvement of Ca2+-permeable cation channels in the cellular uptake of U.
High-affinity iron and calcium transport pathways are involved in U(VI) uptake in the budding yeast Saccharomyces cerevisiae
Authors: Revel Benoît , Catty Patrice , Ravanel Stéphane , Bourguignon Jacques , Alban Claude 
Published: June 2021

AbstractUranium (U) is a naturally-occurring radionuclide toxic for living organisms that can take it up. To date, the mechanisms of U uptake are far from being understood. Here, we used the yeast Saccharomyces cerevisiae as a unicellular eukaryote model to identify U assimilation pathways. Thus, we have identified, for the first time, transport machineries capable of transporting U in a living organism. First, we evidenced a metabolism-dependent U transport in yeast. Then, competition experiments with essential metals allowed us to identify calcium, iron and copper entry pathways as potential routes for U uptake. The analysis of various metal transport mutants revealed that mid1Δ, cch1Δ and ftr1Δ mutants, affected in calcium (Mid1/Cch1 channel) and Fe(III) (Ftr1/Fet3 complex) transport, respectively, exhibited highly reduced U uptake rates and accumulation, demonstrating the implication of these import systems in U uptake. Finally, expression of the Mid1 gene into the mid1Δ mutant restored U uptake levels of the wild type strain, underscoring the central role of the Mid1/Cch1 calcium channel in U absorption process in yeast. Our results also open up the opportunity for rapid screening of U-transporter candidates by functional expression in yeast, before their validation in more complex higher eukaryote model systems.HighlightsLiving yeast Saccharomyces cerevisiae is able to take up UAvailability of a metabolizable substrate stimulates U uptakeCalcium, iron and copper inhibit U uptakeStrains deleted in Mid1/Cch1 calcium channel and Ftr1 iron permease are affected in U uptakeExpression of MID1 gene in mid1Δ strain restore wild type levels of U uptakeGraphical Abstract
The Consciousness Theories Studies (ConTraSt) database: analyzing and comparing empirical studies of consciousness theories
Authors: Yaron Itay , Melloni Lucia , Pitts Michael , Mudrik Liad 
Published: June 2021

AbstractUnderstanding how consciousness arises from neural activity remains one of the biggest challenges for neuroscience. Numerous theories have been proposed in recent years, each gaining independent empirical support. Currently, there is no comprehensive, quantitative and theory-neutral overview of the field that enables an evaluation of how theoretical frameworks interact with empirical research. We provide a bird’s eye view on studies that interpreted their findings in light of at least one of four leading neuroscientific theories of consciousness (N=412 experiments), asking how methodological choices of the researchers might affect the final conclusions. We found that supporting a specific theory can be predicted solely from methodological choices, irrespective of findings. Furthermore, most studies interpret their findings post-hoc, rather than a-priori testing critical predictions of the theories. Our results highlight challenges for the field and provide researchers with a unique, open-access website to further analyze trends in the neuroscience of consciousness.
The dynamic properties of a nuclear coactivator binding domain are evolutionarily conserved
Authors: Karlsson Elin , Sorgenfrei Frieda A. , Andersson Eva , Dogan Jakob , Jemth Per , Chi Celestine N. 
Published: June 2021

ABSTRACTEvolution of proteins is constrained by their structure and function. While there is a consensus that the plasticity of intrinsically disordered proteins relaxes the structural constraints on evolution there is a paucity of data on the molecular details of these processes. The Nuclear co-activator binding domain (NCBD) from CREB-binding protein is a protein-protein interaction domain, which contains a hydrophobic core but is not behaving as a typical globular domain, and has been desribed as ‘molten-globule like’. The highly dynamic properties of NCBD makes it an interesting model system for evolutionary structure-function investigation of intrinsically disordered proteins. We have here compared the structure and biophysical properties of an ancient version of NCBD present in a bilaterian animal ancestor living around 600 million years ago with extant human NCBD. Using a combination of NMR spectroscopy, circular dichroism and kinetic methods we show that although NCBD has increased its thermodynamic stability, it has retained its dynamic biophysical properties in the ligand-free state in the evolutionary lineage leading from the last common bilaterian ancestor to humans. Our findings suggest that the dynamic properties of NCBD have been maintained by purifying selection and thus are important for its function, which includes mediating several distinct protein-protein interactions.
Shape-restrained modelling of protein-small molecule complexes with HADDOCK
Authors: Koukos Panagiotis I. , Réau Manon , Bonvin Alexandre M. J. J. 
Published: June 2021

AbstractSmall molecule docking remains one of the most valuable computational techniques for the structure prediction of protein-small molecule complexes. It allows us to study the interactions between compounds and the protein receptors they target at atomic detail, in a timely and efficient manner. Here we present a new protocol in HADDOCK, our integrative modelling platform, which incorporates homology information for both receptor and compounds. It makes use of HADDOCK’s unique ability to integrate information in the simulation to drive it toward conformations which agree with the provided data. The focal point is the use of shape restraints derived from homologous compounds bound to the target receptors. We have developed two protocols: In the first, the shape is composed of fake atom beads based on the position of the heavy atoms of the homologous template compound, whereas in the second the shape is additionally annotated with pharmacophore data, for some or all beads. For both protocols, ambiguous distance restraints are subsequently defined between those beads and the heavy atoms of the ligand to be docked. We have benchmarked the performance of these protocols with a fully unbound version of the widely used DUD-E dataset. In this unbound docking scenario, our template/shape-based docking protocol reaches an overall success rate of 81% on 99 complexes, which is close to the best results reported for bound docking on the DUD-E dataset.Table of contents graphic
Enhanced Immunoprecipitation Techniques for the Identification of RNA Binding Protein Partners: CRD-BP interactions in mammary epithelial cells
Authors: Fakhraldeen Saja A. , Berry Scott M. , Beebe David J. , Roopra Avtar , Spiegelman Vladimir S. , Alexander Caroline M. 
Published: June 2021

AbstractRNA binding proteins (RBPs) regulate expression of large cohorts of RNA species to affect programmatic changes in cellular phenotypes. In order to describe the function of RBPs within a cell, it is key to identify their mRNA binding partners. This is often done by cross-linking nucleic acids to RBPs, followed by chemical release of the nucleic acid fragments for analysis. However, this methodology is lengthy, involves complex processing leading to extraordinary losses, requires large amounts of starting materials, and is prone to artifacts due to the labile nature of mRNA. To evaluate potential alternative technologies, we tested “exclusion-based” purification of immunoprecipitates (oil-based IFAST™ or air-based SLIDE™), and report here that these methods can efficiently, rapidly and specifically isolate RBP-RNA complexes with minimal handling. The analysis starts with >100x less material than for techniques that include cross-linking. Depending on the specific antibody used, 50-100% of starting protein is retrieved, allowing the assay of endogenous levels of RBP instead of tagged and over-expressed ectopic proteins. Isolated protein and nucleic acid components are purified and analyzed using standard techniques to provide a comprehensive portrait of RBP complexes. Using exclusion-based techniques, we show that the mRNA binding partners for CRD-BP/IMP1/IGF2BP1/ZBP1 in cultured mammary epithelial cells are enriched in mRNAs important for de-toxifying superoxides (glutathione metabolic enzymes) and other mRNAs encoding mitochondrial proteins.
A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq
Authors: Mudge Jonathan M. , Ruiz-Orera Jorge , Prensner John R. , Brunet Marie A. , Gonzalez Jose Manuel , Magrane Michele , Martinez Thomas , Schulz Jana Felicitas , Yang Yucheng T. , Albà M. Mar , Baranov Pavel V. , Bazzini Ariel , Bruford Elspeth , Martin Maria Jesus , Carvunis Anne-Ruxandra , Chen Jin , Couso Juan Pablo , Flicek Paul , Frankish Adam , Gerstein Mark , Hubner Norbert , Ingolia Nicholas T. , Menschaert Gerben , Ohler Uwe , Roucou Xavier , Saghatelian Alan , Weissman Jonathan , van Heesch Sebastiaan 
Published: June 2021

ABSTRACTRibosome profiling (Ribo-seq) has catalyzed a paradigm shift in our understanding of the translational ‘vocabulary’ of the human genome, discovering thousands of translated open reading frames (ORFs) within long non-coding RNAs and presumed untranslated regions of protein-coding genes. However, reference gene annotation projects have been circumspect in their incorporation of these ORFs due to uncertainties about their experimental reproducibility and physiological roles. Yet, it is indisputable that certain Ribo-seq ORFs make stable proteins, others mediate gene regulation, and many have medical implications. Ultimately, the absence of standardized ORF annotation has created a circular problem: while Ribo-seq ORFs remain unannotated by reference biological databases, this lack of characterisation will thwart research efforts examining their roles. Here, we outline the initial stages of a community-led effort supported by GENCODE / Ensembl, HGNC and UniProt to produce a consolidated catalog of human Ribo-seq ORFs.
Meditation-induced effects on whole-brain structural and effective connectivity
Authors: De Filippi Eleonora , Escrichs Anira , Càmara Estela , Garrido César , Sánchez-Fibla Marti , Gilson Matthieu , Deco Gustavo 
Published: June 2021

AbstractIn the past decades, there has been a growing scientific interest in characterizing neural correlates of meditation training. Nonetheless, the mechanisms underlying meditation remain elusive. In the present work, we investigated meditation-related changes in structural and functional connectivities (SC and FC, respectively). For this purpose, we scanned experienced meditators and control (naive) subjects using magnetic resonance imaging (MRI) to acquire structural and functional data during two conditions, resting-state and meditation (focused attention on breathing). In this way, we aimed to characterize and distinguish both short-term and long-term modifications in the brain’s structure and function. First, we performed a network-based analysis of anatomical connectivity. Then, to analyze the fMRI data, we calculated whole-brain effective connectivity (EC) estimates, relying on a dynamical network model to replicate BOLD signals’ spatio-temporal structure, akin to FC with lagged correlations. We compared the estimated EC, FC, and SC links as features to train classifiers to predict behavioral conditions and group identity. The whole-brain SC analysis revealed strengthened anatomical connectivity across large-scale networks for meditators compared to controls. We found that differences in SC were reflected in the functional domain as well. We demonstrated through a machine-learning approach that EC features were more informative than FC and SC solely. Using EC features we reached high performance for the condition-based classification within each group and moderately high accuracies when comparing the two groups in each condition. Moreover, we showed that the most informative EC links that discriminated between meditators and controls involved the same large-scale networks previously found to have increased anatomical connectivity. Overall, the results of our whole-brain model-based approach revealed a mechanism underlying meditation by providing causal relationships at the structure-function level.
Discovering single-cell eQTLs from scRNA-seq data only
Authors: Ma Tianxing , Li Haochen , Zhang Xuegong 
Published: June 2021

AbstracteQTL studies are essential for understanding genomic regulation. Effects of genetic variations on gene regulation are cell-type-specific and cellular-context-related, so studying eQTLs at a single-cell level is crucial. The ideal solution is to use both mutation and expression data from the same cells. However, current technology of such paired data in single cells is still immature. We present a new method, eQTLsingle, to discover eQTLs only with single cell RNA-seq (scRNA-seq) data, without genomic data. It detects mutations from scRNA-seq data and models gene expression of different genotypes with the zero-inflated negative binomial (ZINB) model to find associations between genotypes and phenotypes at single-cell level. On a glioblastoma and gliomasphere scRNA-seq dataset, eQTLsingle discovered hundreds of cell-type-specific tumor-related eQTLs, most of which cannot be found in bulk eQTL studies. Detailed analyses on examples of the discovered eQTLs revealed important underlying regulatory mechanisms. eQTLsingle is a unique powerful tool for utilizing the huge scRNA-seq resources for single-cell eQTL studies, and it is available for free academic use at https://github.com/horsedayday/eQTLsingle.
Theoretical and methodological milestones in international accounting research: the contributions of Jill L. McKinnon
Authors: Patel Chris , Harrison Graeme 
Published: June 2021

PurposeThis paper chronicles Jill McKinnon's theoretical and methodological contributions to international accounting research generally and socio-cultural research specifically over a 25-year period, 1981–2006. The purposes are: (1) to apprise contemporary and future researchers in international accounting, working with a socio-cultural lens, of a major contributor and contribution to the historical origin and development of that lens; and (2) to revisit and reappraise McKinnon's identification of critical theoretical and methodological cautions to guide future research in international accounting.Design/methodology/approachThe paper provides a historical narrative and contemporary appraisal of: (1) McKinnon's seminal doctoral research into the Japanese system of corporate reporting regulation using a holistic and dynamic socio-cultural model of social systems change; and (2) her contribution to the advancement of cross-cultural international accounting research including her critique of that research leading to the identification of cautions, the recognition and observance of which are critical to the development of contemporary and future research. The narrative is informed by historical context of time and space, and imbued and interwoven with the personal story of McKinnon both as human and humane.FindingsMcKinnon's research invoking holistic theoretical and methodological perspectives provides a continuing template and pathway to guide contemporary and future international accounting researchers and to shape the development of international accounting research. Her career, research and humanity leave a legacy distilled into four themes that serve as counsels for accounting research and researchers; eclecticism of world-view and method choice, rigour, holism and the importance of collegiality with and to the accounting research community.Originality/valueThe paper provides original insights into the personality, career development and research of an important contributor to international accounting research specifically and interdisciplinary research in accounting generally. The paper demonstrates empirically the importance of historical analysis, contextualized by time, space and person, in understanding and informing the present state of international accounting research and, hence, linking past, present and future.
Pathways toward entrepreneurial intention among Malaysian universities’ students
Authors: Bazkiaei Hanieh Alipour , Khan Noor Ullah , Irshad Ateeq-ur-Rehman , Ahmed Adeel 
Published: June 2021

PurposeEntrepreneurship is a vital source of job creation and a key driver in promoting economic growth. The Malaysian government encourages higher educational institutions (HEIs) to develop more competitive and innovative graduates for the economy so that Malaysia achieves high-income nation status by 2025. This study aims to investigate the mediating role of attitude toward entrepreneurship (ATE) in the relationship between key psychological factors, that is, subjective norm (SN), perceived behavior control (PBC), big-five (BF) personality traits, entrepreneurial motivation (EM) and educational factors (EFs) with entrepreneurial intention (EI) among Malaysian university students.Design/methodology/approachThis study used a quantitative design based on a positivist approach. The adopted questionnaire was used as the survey instrument. The primary data were collected from a sample of 251 final-year students in the management field who were enrolled in research-intensive Malaysian universities. Data were analyzed through the structural equation modeling (SEM) technique using AMOS 24 software.FindingsFindings confirmed that the BF personality traits, EM, PBC, SN, ATE and EFs were positively related to EI. Furthermore, ATE mediated the relationship between BF personality traits, EM, PBC, SN, EF, and EI among Malaysian university students.Research limitations/implicationsThis research provides critical insights into the key antecedents, for example, psychological and EFs, in explaining the EI of university students and future graduates. However, results can only be generalized to research-intensive Malaysian universities.Originality/valueThis study investigated the relationship between psychological factors, that is, BF personality traits, EM, PBC, SN and EFs in predicting EI of Malaysian university students. ATE mediated the relationship between BF personality traits, EM, PBC, SN, EF and EI among these students.
Antecedents of organizational citizenship behavior towards the environment in manufacturing organizations: using a structural equation modeling approach
Authors: Khan Noor Ullah , Irshad Ateeq-ur-Rehman , Ahmad Saufi Roselina , Ahmed Adeel 
Published: June 2021

PurposeOrganizations worldwide are integrating sustainability into their operations to reduce the damage they do to the environment and to earn a better reputation in society. Scholars have acknowledged the role of environmental transformational leadership (ETL) in creating pro-environmental behaviors (PEBs). The manufacturing sector has shown interest in accepting an environmental management system (EMS) and fostering a mechanism for what is called perceived support organizational support for the environment (POSE). Voluntary PEBs taking the form of organizational citizenship behavior toward the environment (OCBE) increasingly interests researchers because it is important for the success of the EMS in the manufacturing sector. This study aims to investigate the mediating role of the EMS and POSE in the relationship between ETL and OCBE within ISO14001-certified Malaysian manufacturing firms.Design/methodology/approachA quantitative design was used based on a positivist approach. The data of 216 manufacturing firms were targeted using random probability sampling via a survey questionnaire. Later, the data were analyzed through the structural equation modeling (SEM) method using the SmartPLS 3.3.3 software.FindingsResearch findings confirmed a significant direct positive relationship between ETL and OCBE. Also, they confirmed the mediating role of the EMS and POSE in the relationship between ETL and OCBE among ISO14001-certified Malaysian manufacturing firms.Research limitations/implicationsThis research has vital ramifications for both managers and organizations. Manufacturing firms should modify the traditional OCB towards pro-environmental OCBE using key antecedents, e.g. ETL, EMS and POSE.Originality/valueThe study analyzed the impact of ETL on OCBE through the mediating role of PSOE and the EMS. Here the focus is on the impact of OCBE key antecedents, i.e. ETL, EMS and POSE in predicting OCBE among ISO14001-certified Malaysian manufacturing firms.