bluuebunny/crossref_metadata_2025_split huggingface dataset:
Architecture of the cytoplasmic face of the nuclear pore
Authors: Bley Christopher J. , Nie Si , Mobbs George W. , Petrovic Stefan , Gres Anna T. , Liu Xiaoyu , Mukherjee Somnath , Harvey Sho , Huber Ferdinand M. , Lin Daniel H. , Brown Bonnie , Tang Aaron W. , Rundlet Emily J. , Correia Ana R. , Chen Shane , Regmi Saroj G. , Dasso Mary , Patke Alina , Palazzo Alexander F. , Kossiakoff Anthony A. , Hoelz André 
Published: October 2021

AbstractThe nuclear pore complex (NPC) is the sole bidirectional gateway for nucleocytoplasmic transport. Despite recent progress in elucidating the NPC symmetric core architecture, the asymmetrically decorated cytoplasmic face, essential for mRNA export and a hotspot for nucleoporin-associated diseases, has remained elusive. Here, we report a composite structure of the entire human cytoplasmic face obtained by combining biochemical reconstitution, crystal structure determination, docking into cryo-electron tomographic reconstructions, and physiological validation, accounting for a third of the NPC’s mass. Whereas an evolutionarily conserved ∼540 kDa hetero-hexameric cytoplasmic filament nucleoporin complex is anchored by species-specific motifs above the central transport channel, attachment of the pentameric NUP358 bundles depends on the double-ring arrangement of the coat nucleoporin complex. Our results and the predictive power of our composite structure provide a rich foundation for elucidating the molecular basis of mRNA export and nucleoporin diseases.One sentence summaryAn interdisciplinary analysis established the near-atomic molecular architecture of the cytoplasmic face of the human nuclear pore complex.
Structural determinants in the Staphylococcus aureus derived phenol-soluble modulin α2 peptide required for neutrophil formyl peptide receptor activation
Authors: Viklund Moa , Fredriksson Johanna , Holdfeldt André , Lind Simon , Franzyk Henrik , Dahlgren Claes , Sundqvist Martina , Forsman Huamei 
Published: October 2021

ABSTRACTHighly pathogenic Staphylococcus aureus strains produce phenol-soluble modulins (PSMs), peptides which are formylated N-terminally. Nanomolar concentrations of PSMα2 are recognized by formyl peptide receptor 2 (FPR2), but unlike the prototypic FPR2 agonist WKYMVM, PSMα2 is a biased signaling agonist. A shortened N-terminal PSMα2 variant, consisting of the five N- terminal residues, is selectively recognized by the closely related FPR1, showing that the C- terminal part of PSMα2 confers FPR2 selectivity, while the N-terminal part may interact with the FPR1 binding site. In the present study, a combined pharmacological and genetic approach, involving primary neutrophils and engineered FPR “knock-in” and “knock-out” cells, was used to gain molecular insights into FPR1 and FPR2 recognition of formyl peptides and the receptor downstream signaling induced by these peptides. In comparison to the full-length PSMα2, we show that the peptide in which the N-terminal part of PSMα2 was replaced by fMIFL (an FPR1- selective peptide agonist) potently activates both FPRs for production of superoxide anions and β- arrestin recruitment. A shortened analogue of PSMα2 (PSMα21-12), lacking the nine C-terminal residues activated both FPR1 and FPR2 to produce ROS, whereas β-arrestin recruitment was only mediated through FPR1. However, a single amino acid replacement (Gly-2 to Ile-2) in PSMα21-12 was sufficient to alter FPR2 signaling to include β-arrestin recruitment, highlighting a key role of Gly-2 in conferring FPR2 biased signaling. In conclusion, we provide novel structural insights into FPR1 and FPR2 recognition as well as the signaling induced by interaction with formyl peptides derived from PSMα2, originating from Staphylococcus aureus bacteria.
Somatostatin venom analogs evolved by fish-hunting cone snails: From prey capture behavior to identifying drug leads
Authors: Ramiro Iris Bea. L. , Bjørn-Yoshimoto Walden E. , Imperial Julita S. , Gajewiak Joanna , Watkins Maren , Taylor Dylan , Resager William , Ueberheide Beatrix , Bräuner-Osborne Hans , Whitby Frank G. , Hill Christopher P. , Martin Laurent F. , Patwardhan Amol , Concepcion Gisela P. , Olivera Baldomero M. , Safavi-Hemami Helena 
Published: October 2021

AbstractSomatostatin (SS) is a peptide hormone with diverse physiological roles. By investigating a deep-water clade of fish-hunting cone snails, we show that predator-prey evolution has generated a diverse set of SS analogs, each optimized to elicit specific systemic physiological effects in prey. The increased metabolic stability, distinct SS receptor activation profiles, and chemical diversity of the venom analogs make them suitable leads for therapeutic application, including pain, cancer and endocrine disorders. Our findings not only establish the existence of SS-like peptides in animal venoms, but also serve as a model for the synergy gained from combining molecular phylogenetics and behavioral observations to optimize the discovery of natural products with biomedical potential.One Sentence SummarySomatostatin drug design by fish-hunting cone snails
Diversity, function and evolution of marine microbe genomes
Authors: Chen Jianwei , Guo Yang , Jia Yangyang , Liu Guilin , Li Denghui , Xu Dayou , Wang Bing , Zhou Li , Peng Ling , Zhao Fang , Zhu Yuanfang , Sun Jiahui , Ye Chen , Wang Jun , Zhang He , Liu Shanshan , Seim Inge , Liu Xin , Xu Xun , Yang Huanming ,   GOMP Consortium, Kristiansen Karsten , Fan Guangyi 
Published: October 2021

AbstractTrillions of marine bacterial, archaeal and viral species contribute to the majority diversity of life on Earth. In the current study, we have done a comprehensive review of all the published studies of marine microbiome by re-analyzing most of the available high throughput sequencing data. We collected 17.59 Tb sequencing data from 8,165 metagenomic and prokaryotic samples, and systematically evaluated the genome characters, including genome size, GC content, phylogeny, and the functional and ecological roles of several typical phyla. A genome catalogue of 9,070 high quality genomes and a gene catalogue including 156,209,709 genes were constructed, representing the most integrate marine prokaryotic datasets till now. The genome size of Alphaproteobacteria and Actinobacteria was significant correlated to their GC content. A total of 44,322 biosynthetic gene clusters distributed in 53 types were detected from the reconstructed marine prokaryotic genome catalogue. Phylogenetic annotation of the 8,380 bacterial and 690 archaeal species revealed that most of the known bacterial phyla (99/111), including 62 classes and 181 orders, and four extra unclassified genomes from two candidate novel phyla were detected. In addition, taxonomically unclassified species represented a substantial fraction of 64.56% and 80.29% of the phylogenetic diversity of Bacteria and Archaea respectively. The genomic and ecological features of three groups of Cyanobacteria, luminous bacteria and methane-metabolizing archaea, including inhabitant preference, geolocation distribution and others were through discussed. Our database provides a comprehensive resource for marine microbiome, which would be a valuable reference for studies of marine life origination and evolution, ecology monitor and protection, bioactive compound development.
A system for CBAF reconstitution reveals roles for BAF47 domains and BCL7 in nucleosome ejection
Authors: Mulvihill Timothy S. , Nelson Mary L. , Verma Naveen , Jones Kevin B. , Cairns Bradley R. 
Published: October 2021

ABSTRACTCanonical BAF (CBAF) is an essential 12-protein chromatin-remodeling complex that slides and/or ejects nucleosomes using the alternative catalytic ATP-dependent DNA translocases BRG1 or BRM. Currently, the regulation of BRG1/BRM activity and nucleosome ejection remain incompletely understood. To address this, we developed a system for full CBAF reconstitution and purification, and created a novel nucleosome ejection assay. ARID1A and DPF2 were dispensable for assembly and chromatin remodeling activity, contrasting with prior work. The actin-related protein BAF53A and β-actin components interacted and enhanced DNA translocation, and were required for BCL7A incorporation, which potentiated ejection. BAF47 also regulated ejection, utilizing two stimulatory domains and an autoinhibitory domain. Finally, we provide evidence for ‘direct’ nucleosome ejection at low nucleosome density on closed circular arrays. Taken together, we provide powerful new tools for CBAF mechanistic investigation and reveal new roles for several CBAF components.
Application of sequence semantic and integrated cellular geography approach to study biogenesis of exonic circular RNA
Authors: Kumar Rajnish , Lahiri Tapobrata , Pal Manoj Kumar 
Published: October 2021

AbstractBackgroundConcurrent existence of lncRNA and circular RNA at both nucleus and cytosol within a cell at different proportion is well reported. Secondly, information on genes transcribing both circular and lncRNAs along with total number of RBP binding sites for both of these RNA types is extractable from databases. This study showed how these apparently unconnected pieces of reports could be put together to build a model leading to biogenesis of circular RNA.ResultsAs a result of this study, a model was built under the premises that, sequences with special semantics were molecular precursors in biogenesis of circular RNA which occurred through catalytic role of some specific RBPs. The model outcome was further strengthened by fulfillment of three logical lemmas which were extracted and assimilated in this work using a novel data analytic approach, Integrated Cellular Geography. Result of the study was found to be in well agreement with proposed model. Furthermore this study also indicated that biogenesis of circular RNA was a post-transcriptional event.ConclusionsOverall, this study provides a novel systems biology based model under the paradigm of Integrated Cellular Geography which can assimilate independently performed experimental results and data published by global researchers on RNA biology to provide important information on biogenesis of exonic circular RNAs considering lncRNAs as precursor molecule.
Extracellular loop 2 of G protein-coupled olfactory receptors is critical for odorant recognition
Authors: Yu Yiqun , Pacalon Jody , Ma Zhenjie , Xu Lun , Belloir Christine , Topin Jeremie , Briand Loïc , Golebiowski Jérôme , Cong Xiaojing 
Published: October 2021

AbstractG protein-coupled olfactory receptors (ORs) enable us to detect innumerous odorants. They are also ectopically expressed, emerging as attractive drug targets. ORs can be promiscuous or highly specific, which is part of Nature’s strategy for odor discrimination. This work demonstrates that the extracellular loop 2 (ECL2) plays critical roles in OR promiscuity and specificity. Using site-directed mutagenesis and molecular modeling, we constructed 3D OR models in which ECL2 forms a lid of the orthosteric pocket. ECL2 controls the shape and the volume of the odorant-binding pocket, maintains the pocket hydrophobicity and acts as a gatekeeper of odorant binding. The interplay between the specific orthosteric pocket and the variable, less specific ECL2 controls OR specificity and promiscuity. The 3D models enabled virtual screening of new OR agonists and antagonists, exhibiting 78% hit rate in cell assays. This approach can be generalized to structure-based ligand screening for other GPCRs that lack high-resolution 3D structures.
Geological processes mediate a subsurface microbial loop in the deep biosphere
Authors: Gittins Daniel A. , Desiage Pierre-Arnaud , Morrison Natasha , Rattray Jayne E. , Bhatnagar Srijak , Chakraborty Anirban , Zorz Jackie , Li Carmen , Horanszky Oliver , Cramm Margaret A. , Webb Jamie , MacDonald Adam , Fowler Martin , Campbell D. Calvin , Hubert Casey R. J. 
Published: October 2021

Summary paragraphThe deep biosphere is the largest microbial habitat on Earth and features abundant bacterial endospores1,2. Whereas dormancy and survival at theoretical energy minima are hallmarks of subsurface microbial populations3, the roles of fundamental ecological processes like dispersal and selection in these environments are poorly understood4. Here we combine geophysics, geochemistry, microbiology and genomics to investigate biogeography in the subsurface, focusing on bacterial endospores in a deep-sea setting characterized by thermogenic hydrocarbon seepage. Thermophilic endospores in permanently cold seabed sediments above petroleum seep conduits were correlated with the presence of hydrocarbons, revealing geofluid-facilitated cell migration pathways originating in deep oil reservoirs. Genomes of thermophilic bacteria highlight adaptations to life in anoxic petroleum systems and reveal that these dormant populations are closely related to oil reservoir microbiomes from around the world. After transport out of the subsurface and into the deep-sea, thermophilic endospores re-enter the geosphere by sedimentation. Viable thermophilic endospores spanning the top several metres of the seabed correspond with total endospore counts that are similar to or exceed the global average. Burial of dormant cells enables their environmental selection in sedimentary formations where new petroleum systems establish, completing a geological microbial loop that circulates living biomass in and out of the deep biosphere.
Notch signaling determines cell-fate specification of the two main types of vomeronasal neurons of rodents
Authors: Katreddi Raghu Ram , Taroc Ed Zandro M. , Hicks Sawyer M , Lin Jennifer M , Liu Shuting , Xiang Mengqing , Forni Paolo E. 
Published: October 2021

AbstractThe ability of terrestrial vertebrates to find food, mating partners and to avoid predators heavily relies on the detection of chemosensory information from the environment. The olfactory system of most vertebrate species comprises two distinct chemosensory systems usually referred to as the main and the accessory olfactory system. Olfactory sensory neurons of the main olfactory epithelium detect and transmit odor information to main olfactory bulb (MOB), while the chemosensory neurons of the vomeronasal organ detect semiochemicals responsible for social and sexual behaviors and transmit information to the accessory olfactory bulb (AOB). The vomeronasal sensory epithelium (VNE) of most mammalian species contains uniform vomeronasal (VN) system with vomeronasal sensory neurons (VSNs) expressing vomeronasal receptors of the V1R family. However, rodents and some marsupials have developed a more complex binary VN system, where VNO containing a second main type of VSNs expressing vomeronasal receptors of the V2R family is identified. In mice, V1R and V2R VSNs form from a common pool of progenitors but have distinct differentiation programs. As they mature, they segregate in different regions of the VNE and connect with different parts of the AOB. How these two main types of VSNs are formed has never been addressed. In this study, using single cell RNA sequencing data, we identified differential expression of Notch1 receptor and Dll4 ligand among the neuronal precursors at the VSN dichotomy. We further demonstrated with loss of function (LOF) and gain of function (GOF) studies that Dll4-Notch1 signaling plays a crucial role in triggering the binary dichotomy between the two main types of VSNs in mice.Graphical Abstract
An examination of board diversity and corporate social responsibility disclosure: evidence from banking sector in the Arabian Gulf countries
Authors: Issa Ayman , Zaid Mohammad A.A. , Hanaysha Jalal Rajeh , Gull Ammar Ali 
Published: October 2021

PurposeThe purpose of this study is to examine the impact of board diversity (e.g. education, gender, nationality and royal family members) on voluntary corporate social responsibility (CSR) disclosure for a sample of banks listed in the Arabian Gulf Council countries.Design/methodology/approachThe authors use the Global Reporting Initiative guidelines to construct the CSR disclosure index. The empirical analysis is based on the data of banks listed in the Gulf Cooperation Council countries over the period 2011–2019. To tackle the potential issue of endogeneity, the authors apply the system generalized method of moments (GMM) estimation approach to investigate the relationship between board diversity and CSR disclosure index.FindingsThe findings of the analysis show that there is a significant relationship between board diversity and the level of voluntary CSR disclosure. Specifically, the authors find that diversity captured by the education level, nationality and the presence of royal family members on board is positively associated with the level of voluntary CSR disclosure while diversity captured by the gender of board members is negatively associated with the level of voluntary CSR disclosure.Practical implicationsThe regulators, policymakers, stakeholders and the board of directors become aware of the diversity mechanisms that must be used to promote CSR practices in the banking sector of Arabian Gulf countries.Originality/valueThe authors extend the existing literature by providing empirical evidence on the association between board diversity and voluntary CSR disclosure practices of banks operating in the Arabian Gulf countries. This study also highlights that board gender diversity may have a different impact on voluntary CSR disclosure between developed countries and developing countries. This paper also provides preliminary evidence on the importance of education level, the presence of foreign and royal directors on board to influence CSR practices of banks operating in the Arabian Gulf countries.
Designing innovative jobs: a fuzzy-set configurational analysis of job characteristics
Authors: Cangialosi Nicola , Battistelli Adalgisa , Odoardi Carlo 
Published: October 2021

PurposeHow to design jobs to support innovation is an issue that has received plenty of consideration over the past years. Building on the job characteristics model, the present study is set up to identify configurations of perceived job characteristics for innovation.Design/methodology/approachBy adopting a fuzzy-set configurational approach (fsQCA), the research question is addressed through a two-wave self-report survey of 199 employees of an Italian manufacturing company.FindingsResults reveal four compatible configurations of job characteristics leading to high levels of innovative work behavior and two for low levels.Practical implicationsThe results offer guidance for managers and organizations that aim to strengthen employee-driven innovation by offering different recipes of job design to maximize the chance of boosting innovative behaviors among their workers.Originality/valueThis research is one of the first to empirically test the relation of job characteristics for innovative behavior using a configurational approach. By doing so it contributes to the literature by advancing the notion that innovative endeavors are determined by the holistic effects of different interdependent configurations of job characteristics.
Hindsight is 2020: identifying missed leadership opportunities to reduce employee turnover intention amid the COVID-19 shutdown
Authors: Robertson Melva B. 
Published: October 2021

Purpose
The purpose of this paper is to highlight how organizational leaders influenced the high 2021 turnover rates amid the COVID-19 shutdown.

Design/methodology/approach
This paper explores several factors that contributed to employee turnover intention before the pandemic and how unresolved leadership behaviors and toxic organizational cultures exacerbated circumstances that led to what is now known as The Great Resignation of 2021.

Findings
This paper suggests that while the pandemic shutdown temporarily paused employee turnover, organizational leaders missed an opportunity to retain their employees by not recognizing and changing factors that led to pre-existing employee turnover intention.

Originality/value
This paper explores solutions to help leaders support and retain current and future employees as the pandemic continues and in the event of futures crises. It offers recommendations for leadership development support to help strengthen leaders in their highly complex roles.
Broadband seismic source data acquisition and processing to delineate iron oxide deposits in the Blötberget mine‐central Sweden
Authors: Pertuz Tatiana , Malehmir Alireza , Bos Jordan , Brodic Bojan , Ding Yinshuai , de Kunder Richard , Marsden Paul 
Published: October 2021

ABSTRACTA prototype electromagnetic vibrator, referred to here as E‐Vib, was upgraded and developed for broadband hardrock and mineral exploration seismic surveys. We selected the iron oxide mine in Blötberget, central Sweden, for a test site in 2019 for the newly developed E‐Vib because of the availability of earlier seismic datasets (from 2015 to 2016) for verification of its performance for hardrock imaging purposes. The two‐dimensional data acquisition consisted of a fixed geometry with 550 receiver locations spaced at every 5 m, employing both cabled and wireless seismic recorders, along an approximately 2.7 km long profile. The E‐Vib operated at every second receiver station (i.e. 10 m spacing) with a linear sweep of 2–180 Hz and with a peak force of 7 kN. The processing workflow took advantage of the broadband signal generated by the E‐Vib in this challenging hardrock environment with varying ground conditions. The processed seismic section shows a set of reflections associated with the known iron oxide mineralization and a major crosscutting reflection interpreted to be from a fault system likely to be crosscutting the mineralization. The broadband source data acquisition and subsequent processing helped to improve signal quality and resolution in comparison with the earlier workflows and data where a drophammer seismic source was used as the seismic source. These results suggest new possibilities for the E‐Vib source for improved targeting in hardrock geological settings.