bluuebunny/crossref_metadata_2025_split huggingface dataset:
Landscapes associated with Japanese encephalitis virus reflect the functional biogeography of waterbird species across Australia and the Central Indo-Pacific region
Authors: Walsh Michael G. , Webb Cameron , Brookes Victoria 
Published: August 2023

AbstractJapanese encephalitis virus (JEV), a zoonotic, mosquito-borne virus, has broad circulation across the Central Indo-Pacific biogeographical region (CIPBR), which recently expanded dramatically within this region across southeastern Australia over the summer of 2021-2022. Preliminary investigation of the landscape epidemiology of the outbreaks of JEV in Australian piggeries found associations with particular landscape structure as well as ardeid species richness. The ways in which waterbird species from diverse taxonomic pools with substantial functional variation might couple with JEV-associated landscape structure was not explored, and therefore, key questions regarding the landscape epidemiology and infection ecology of JEV remain unanswered. Moreover, given the established presence of JEV within the CIBPR, the extent to which waterbird species pools in JEV-associated landscapes in Australia reflect broader regional patterns in functional biogeography presents a further knowledge gap particularly with respect to potential virus dispersal via maintenance hosts. The current study investigated waterbird species presence, ecological traits, and functional diversity distribution at landscape scale, and how these aligned with confirmed JEV detections in eastern Australia and the wider CIPBR. The results showed that waterbird habitat associated with JEV detection in Australia in 2022 and more widely across the CIPBR over the last 20 years reflects a range of species representing 8 families in 4 orders (ardeids, anatids, rallids, phalacrocoracids, threskiornithids, gruids, and pelecanids). Increasing waterbird functional diversity (trait-based mean pairwise dissimilarity) was associated with landscapes delineating JEV occurrence, while only one individual trait, high hand-wing index, was consistently associated with species presence in these JEV-associated landscapes in both Australia and the broader CIPBR. This suggests that dispersal capacity among the waterbird species pools that dominate JEV-associated landscapes might be important. By taking an agnostic approach to JEV maintenance host status, this study indicates a relatively large, CIPBR-wide pool of waterbird families associated with JEV landscapes, challenging the narrow view that JEV maintenance is limited to ardeid birds. In addition, these findings highlight the potential for leveraging functional biogeography in high-risk landscapes across broad geographic extent to guide landscape-specific selection of species for JEV surveillance.
Cooperation between bacteriocytes and endosymbionts drives function and development of symbiotic cells in mussel holobionts
Authors: Chen Hao , Li Mengna , Zhong Zhaoshan , Wang Minxiao , Lian Chao , Han Guanghui , Wang Hao , Zhou Li , Zhang Huan , Cao Lei , Li Chaolun 
Published: August 2023

AbstractSymbiosis drives the adaptation and evolution in multicellular organisms. Modeling the function and development of symbiotic cells/organs in holobionts is yet challenging. Here, we surveyed the molecular function and developmental trajectory of bacteriocyte lineage in non-model deep-sea mussels by constructing a high-resolution single-cell expression atlas of gill tissue. We show that mussel bacteriocytes optimized immune processes to facilitate recognition, engulfment, and elimination of endosymbionts, and interacted with them intimately in sterol, carbohydrate, and ammonia metabolism. Additionally, the bacteriocytes could arise from three different stem cells as well as bacteriocytes themselves. In particular, we showed that the molecular functions and developmental process of bacteriocytes were guided by the same set of regulatory networks and dynamically altered regarding to symbiont abundance via sterol-related signaling. The coordination in the functions and development of bacteriocytes and between the host and symbionts underlies the interdependency of symbiosis, and drives the deep-sea adaptation of mussels.
Mentoring practices predictive of doctoral student outcomes in a biological sciences cohort
Authors: Debray Reena , Dewald-Wang Emily A. , Ennis Katherine K. 
Published: August 2023

AbstractDespite the importance of a diversity of backgrounds and perspectives in biological research, women, racial and ethnic minorities, and students from non-traditional academic backgrounds remain underrepresented in the composition of university faculty. Through a study on doctoral students at a research-intensive university, we pinpoint advising from faculty as a critical component of graduate student experiences and productivity. Graduate students from minority backgrounds reported lower levels of support from their advisors and research groups. However, working with an advisor from a similar demographic background substantially improved productivity and well-being of these students. Several other aspects of mentoring practices positively predicted student success and belonging, including frequent one-on-one meetings, empathetic and constructive feedback, and relationships with other peer or faculty mentors. Our study highlights the need to renovate graduate education with a focus on retention – not just recruitment – to best prepare students for success in scientific careers.
13C-SpaceM: Spatial single-cell isotope tracing reveals heterogeneity ofde novofatty acid synthesis in cancer
Authors: Buglakova Elena , Ekelöf Måns , Schwaiger-Haber Michaela , Schlicker Lisa , Molenaar Martijn R. , Mohammed Shahraz , Stuart Lachlan , Eisenbarth Andreas , Hilsenstein Volker , Patti Gary J. , Schulze Almut , Snaebjornsson Marteinn T. , Alexandrov Theodore 
Published: August 2023

AbstractMetabolism has emerged as a key factor in homeostasis and disease including cancer. Yet, little is known about the heterogeneity of metabolic activity of cancer cells due to the lack of tools to directly probe it. Here, we present a novel method,13C-SpaceM for spatial single-cell isotope tracing of glucose-dependentde novolipogenesis. The method combines imaging mass spectrometry for spatially-resolved detection of13C6-glucose-derived13C label incorporated into esterified fatty acids with microscopy and computational methods for data integration and analysis. We validated13C-SpaceM on a spatially-heterogeneous normoxia-hypoxia model of liver cancer cells. Investigating cultured cells, we revealed single-cell heterogeneity of lipogenic acetyl-CoA pool labelling degree upon ACLY knockdown that is hidden in the bulk analysis and its effect on synthesis of individual fatty acids. Next, we adapted13C-SpaceM to analyze tissue sections of mice harboring isocitrate dehydrogenase (IDH)-mutant gliomas. We found a strong induction ofde novofatty acid synthesis in the tumor tissue compared to the surrounding brain. Comparison of fatty acid isotopologue patterns revealed elevated uptake of mono-unsaturated and essential fatty acids in the tumor. Furthermore, our analysis uncovered substantial spatial heterogeneity in the labelling of the lipogenic acetyl-CoA pool indicative of metabolic reprogramming during microenvironmental adaptation. Overall,13C-SpaceM enables novel ways for spatial probing of metabolic activity at the single cell level. Additionally, this methodology provides unprecedented insight into fatty acid uptake, synthesis and modification in normal and cancerous tissues.
eQTL mapping in transgenic alpha-synuclein carryingCaenorhabditis elegansrecombinant inbred line
Authors: Huang Yuqing , Wang Yiru A. , van Sluijs Lisa , Vogels Demi H. J. , Chen Yuzhi , Tegelbeckers Vivian I. P. , Schoonderwoerd Steven , Riksen Joost A.G. , Kammenga Jan E. , Harvey Simon C. , Sterken Mark G. 
Published: August 2023

AbstractProtein aggregation of α-synuclein (αS) is a genetic and neuropathological hallmark of Parkinson’s disease (PD). Studies in the model nematodeCaenorhabditis eleganssuggested that variation of αS aggregation depends on the genetic background. However, which genes and genetic modifiers underlie individual differences in αS pathology remains unknown. To study the genotypic-phenotypic relationship of αS aggregation, we constructed a Recombinant Inbred Line (RIL) panel derived from a cross between genetically divergent strainsC. elegansNL5901 and SCH4856, both harboring the human αS gene. As a first step to discover genetic modifiers 70 αS-RILs were measured for whole-genome gene expression and expression quantitative locus analysis (eQTL) were mapped. We detected multiple eQTL hot-spots, many of which were located on Chromosome V. To confirm a causal locus, we developed Introgression Lines (ILs) that contain SCH4856 introgressions on Chromosome V in an NL5901 background. We detected 74 genes with an interactive effect between αS and the genetic background, including the human p38 MAPK homologuepmk-1that has previously been associated with PD. Together, we present a unique αS-RIL panel for defining effects of natural genetic variation on αS pathology, which contributes to finding genetic modifiers of PD.
Tip60-mediated Rheb acetylation links palmitic acid with mTORC1 activation and insulin resistance
Authors: Zhao Zengqi , Chen Qiang , Xiang Xiaojun , Dai Weiwei , Fang Wei , Cui Kun , Li Baolin , Liu Qiangde , Liu Yongtao , Shen Yanan , Li Yueru , Xu Wei , Mai Kangsen , Ai Qinghui 
Published: August 2023

AbstractDifferences in dietary fatty acid saturation impact glucose homeostasis and insulin sensitivity in vertebrates. Excess dietary intake of saturated fatty acids (SFAs) induces glucose intolerance and metabolic disorders. In contrast, unsaturated fatty acids (UFAs) elicit beneficial effects on insulin sensitivity. However, it remains elusive how SFAs and UFAs signal differentially toward insulin signaling to influence glucose homeostasis. Here, using a croaker model, we report that dietary palmitic acid (PA), but not oleic acid or linoleic acid, leads to dysregulation of mTORC1 signaling which provokes systemic insulin resistance and glucose intolerance. Mechanistically, using croaker primary myocytes, mouse C2C12 myotubes and HEK293T cells, we show that PA-induced mTORC1 activation is dependent on mitochondrial fatty acid β oxidation. Notably, PA profoundly elevates acetyl-CoA derived from mitochondrial fatty acid β oxidation which intensifies Tip60-mediated Rheb acetylation. Subsequently, the induction of Rheb acetylation facilitates hyperactivation of mTORC1 which enhances serine phosphorylation of IRS1 and simultaneously inhibits transcription of IRS1 through impeding TFEB nuclear translocation, leading to impairment of insulin signaling. Furthermore, targeted abrogation of acetyl-CoA produced from fatty acid β oxidation or Tip60-mediated Rheb acetylation by pharmacological inhibition and genetic knockdown rescues PA-induced insulin resistance. Collectively, this study reveals a conserved acetylation-dependent mechanistic insight for understanding the link between fatty acids and insulin resistance, which may provide a potential therapeutic avenue to intervene in the development of T2D.
Using a Deep Generation Network Reveals Neuroanatomical Specificity in Hemispheres
Authors: Wang Gongshu , Jiang Ning , Ma Yunxiao , Yan Tianyi 
Published: August 2023

AbstractAsymmetry is an important property of brain organization, but its nature is still poorly understood. Capturing the neuroanatomical components specific to each hemisphere facilitates the understanding of the establishment of brain asymmetry. Since deep generative networks (DGNs) have powerful inference and recovery capabilities, we use one hemisphere to predict the opposite hemisphere by training the DGNs, which automatically fit the built-in dependencies between the left and right hemispheres. After training, the reconstructed images approximate the homologous components in the hemisphere. We use the difference between the actual and reconstructed hemispheres to measure hemisphere-specific components due to asymmetric expression of environmental and genetic factors. The results show that our model is biologically plausible and that our proposed metric of hemispheric specialization is reliable, representing a wide range of individual variation. Together, this work provides promising tools for exploring brain asymmetry and new insights into self-supervised DGNs for representing the brain.
Nanopores reveal the stoichiometry of single oligo-adenylates produced by type III CRISPR-Cas
Authors: Fuentenebro-Navas David , Steens Jurre A. , de Lannoy Carlos , Noordijk Ben , de Ridder Dick , Staals Raymond H.J. , Schmid Sonja 
Published: August 2023

AbstractCyclic oligoadenylates (cOAs) are small second messenger molecules produced by the type III CRISPR-Cas system as part of the prokaryotic immune response. The role of cOAs is to allosterically activate downstream effector proteins that induce dormancy or cell death, and thus abort viral spread through the population. Interestingly, different type III systems have been reported to utilize different cOA stoichiometries (with 3 to 6 adenylate monophosphates). However, so far, their characterization has only been possible in bulk and with sophisticated equipment, while a portable assay with single-molecule resolution has been lacking. Here, we demonstrate the label-free detection of single cOA molecules using a simple protein nanopore assay. It sensitively identifies the stoichiometry of individual cOA molecules and their mixtures from synthetic and enzymatic origin. To achieve this, we trained a convolutional neural network (CNN) and validated it with a series of experiments on mono- and polydisperse cOA samples. Ultimately, we determined the stoichiometric composition of cOAs produced enzymatically by the CRISPR type III-A and III-B variants ofThermus thermophilus. Interestingly, both variants produce cOAs of nearly identical composition, and we discuss the biological implications of this finding. The presented nanopore-CNN workflow with single-cOA resolution can be adapted to many other signaling molecules (including eukaryotic ones), and it may be integrated into portable handheld devices with potential point-of-care applications.
Integrative assessment of total and intact HIV-1 reservoir by a five-region multiplexed Rainbow digital PCR assay
Authors: Delporte Mareva , van Snippenberg Willem , Blomme Evy E. , Rutsaert Sofie , Verschoore Maxime , De Smet Evelien , De Scheerder Marie-Angélique , Gerlo Sarah , Vandekerckhove Linos , Trypsteen Wim 
Published: August 2023

AbstractPersistent latent reservoirs of intact HIV-1 proviruses, capable of rebounding despite suppressive ART, hinder efforts towards an HIV-1 cure. Hence, assays specifically quantifying intact proviruses are crucial to assess the impact of curative interventions. Clinical trials have utilized two recent assays: intact proviral DNA assay (IPDA) and Q4PCR. While IPDA is more sensitive due to amplifying short fragments, it may overestimate intact fractions by relying only on two small regions. Q4PCR is sequencing-based and its performance might be subjected to bias against full-length proviruses. Leveraging digital PCR (dPCR) advancements, we developed the ‘Rainbow’ 5-plex proviral HIV-1 DNA assay, assessing it with standard materials and samples from 69 PLWH. The Rainbow assay proved equally sensitive but more specific than IPDA, is not subjected to bias against full-length proviruses, enabling high-throughput quantification of total and intact reservoir size. This innovation offers potential for targeted evaluation and monitoring of rebound-competent reservoirs, contributing to HIV-1 management and cure strategies.TeaserThe 5 color ‘HIV-1 Rainbow’ digital PCR assay offers a multi-level view on the HIV reservoir in one snapshot reaction.
Russula(Basidiomycota, Russulales, Russulaceae) subsect.Roseinae“down under”
Authors: Buyck Bart , Horak Egon , Cooper Jerry A. , Song Yu 
Published: August 2023

AbstractThe present contribution presents species ofRussulasubsect.RoseinaeSarnari from the southern hemisphere.Russula incrustataBuyck, sp. nov. andR. koniamboensisBuyck, sp. nov. are described from New Caledonia,R. purpureotinctaR. F. R. McNabb from New Zealand is redescribed in detail and two secotioid species,R. albobrunneaT. Lebel from Australia andR. kermesina(R. F. R. McNabb) T. Lebel from New Zealand are shown to be the first known secotioid taxa inRoseinae. The systematic placement and importance of these southern taxa is discussed.
Infralimbic parvalbumin neural activity facilitates cued threat avoidance
Authors: Ho Yi-Yun , Yang Qiuwei , Boddu Priyanka , Bulkin David A. , Warden Melissa R. 
Published: August 2023

ABSTRACTThe infralimbic cortex (IL) is essential for flexible behavioral responses to threatening environmental events. Reactive behaviors such as freezing or flight are adaptive in some contexts, but in others a strategic avoidance behavior may be more advantageous. IL has been implicated in avoidance, but the contribution of distinct IL neural subtypes with differing molecular identities and wiring patterns is poorly understood. Here, we study IL parvalbumin (PV) interneurons in mice as they engage in active avoidance behavior, a behavior in which mice must suppress freezing in order to move to safety. We find that activity in inhibitory PV neurons increases during movement to avoid the shock in this behavioral paradigm, and that PV activity during movement emerges after mice have experienced a single shock, prior to learning avoidance. PV neural activity does not change during movement toward cued rewards or during general locomotion in the open field, behavioral paradigms where freezing does not need to be suppressed to enable movement. Optogenetic suppression of PV neurons increases the duration of freezing and delays the onset of avoidance behavior, but does not affect movement toward rewards or general locomotion. These data provide evidence that IL PV neurons support strategic avoidance behavior by suppressing freezing.
BioE3 enables the identification ofbona fidetargets of E3 ligases
Authors: Barroso-Gomila Orhi , Merino-Cacho Laura , Muratore Veronica , Perez Coralia , Taibi Vincenzo , Maspero Elena , Azkargorta Mikel , Iloro Ibon , Trulsson Fredrik , Vertegaal Alfred C. O. , Mayor Ugo , Elortza Felix , Polo Simona , Barrio Rosa , Sutherland James D. 
Published: August 2023

ABSTRACTThe post-translational modification of proteins by ubiquitination is a highly regulated process that involves a dynamic, three-step enzymatic cascade, where more than 600 E3 ligases play a critical role in recognizing specific substrates for modification. Separatingbona fidetargets of E3s from E3-interacting proteins remains a major challenge in the field. In this study, we present BioE3, a novel approach for identifying substrates of ubiquitin-like (UbL) E3 ligases of interest. Using BirA-E3 ligase fusion proteins and bioUbLs, the method facilitates site-specific biotinylation of UbL-modified substrates of particular E3s for proteomic identification. We demonstrate that the BioE3 system can identify both known and novel targets of two RING-type ubiquitin E3 ligases: RNF4, known to be involved in DNA damage response and the regulation of PML nuclear bodies, and MIB1, implicated in endocytosis, autophagy, and centrosomal protein homeostasis. We further show the versatility of BioE3 by identifying targets of an organelle-specific E3 (MARCH5) and a relatively uncharacterized E3 (RNF214). Furthermore, we show that BioE3 works with HECT-type E3 ligases and identify novel targets of NEDD4 involved in vesicular trafficking. BioE3 is a powerful tool that enables identification ofbona fidesubstrates of UbL E3 ligases and how they change with chemical perturbations. BioE3 may also be applicable for UbLs beyond Ub and SUMO, as well as other E3 ligase classes. The resulting knowledge can shed light on the regulation of cellular processes by the complex UbL network and provide information useful for strategies such as targeted protein degradation (TPD), advancing our understanding of fundamental biological mechanisms and their applications.
The apoptotic, inflammatory, and fibrinolytic actions of vasoinhibin are in a motif different from its antiangiogenic HGR motif
Authors: Robles Juan Pablo , Zamora Magdalena , Garcia-Rodrigo Jose F. , Perez Alma Lorena , Bertsch Thomas , Martinez de la Escalera Gonzalo , Triebel Jakob , Clapp Carmen 
Published: August 2023

AbstractVasoinhibin is a proteolytic fragment of the hormone prolactin that inhibits blood vessel growth (angiogenesis) and permeability, stimulates the apoptosis and inflammation of endothelial cells and promotes fibrinolysis. The antiangiogenic and antivasopermeability properties of vasoinhibin were recently traced to the HGR motif located in residues 46 to 48, allowing the development of potent, orally active, HGR-containing vasoinhibin analogs for therapeutic use against angiogenesis-dependent diseases. However, whether the HGR motif is also responsible for the apoptotic, inflammatory, and fibrinolytic properties of vasoinhibin has not been addressed. Here, we report that HGR-containing analogs are devoid of these properties. Instead, the incubation of human umbilical vein endothelial cells with oligopeptides containing the sequence HNLSSEM, corresponding to residues 30 to 36 of vasoinhibin, induced apoptosis, the nuclear translocation of NF-κB, the expression of genes encoding leukocyte adhesion molecules (VCAM1andICAM1) and proinflammatory cytokines (IL1B, IL6, TNF), and the adhesion of peripheral blood leukocytes. Also, the intravenous or intra-articular injection of HNLSSEM-containing oligopeptides induced the expression ofVcam1, Icam1, Il1b, Il6, Tnfin the lung, liver, kidney, eye, and joints of mice and, like vasoinhibin, these oligopeptides promoted the lysis of plasma fibrin clots by binding to plasminogen activator inhibitor-1 (PAI-1). Moreover, the inhibition of PAI-1, urokinase plasminogen activator receptor, or NF-κB prevented the apoptotic and inflammatory actions. In conclusion, the functional properties of vasoinhibin are segregated into two different structural determinants. Because apoptotic, inflammatory, and fibrinolytic actions may be undesirable for antiangiogenic therapy, HGR-containing vasoinhibin analogs stand as selective and safe agents for targeting pathological angiogenesis.
Effects of information on salary satisfaction during the COVID-19 pandemic: an equity-based mediation model
Authors: Montalvo-Arroyo Sandra , de la Torre-Ruiz José Manuel , Vidal-Salazar María Dolores , Cordón-Pozo Eulogio 
Published: August 2023

PurposeThis research aims to study the effects of information (on salary, salary reductions and the pandemic's impact on the organization) on the salary satisfaction of workers whose salary had been cut during the coronavirus disease 2019 (COVID-19) pandemic, analyzing the mediating role of salary equity in this relationship.Design/methodology/approachInformation was acquired with a structured questionnaire sent by email in May 2021 from 251 employees in Spain during the “third wave” of COVID-19. The model was estimated using the weighted least squares mean and variance adjusted (WLSMV).FindingsResults collected reveal that workers' perceptions of equity fully mediated the relationship between salary information, information on salary cuts and salary satisfaction.Practical implicationsLearning more about the effects of information on salary satisfaction can contribute to communication policies that reduce the negative impact of sensitive salary decisions, practical implications for employees, organizations and policymakers.Originality/valueThis study examines the central role of organizational information as a mechanism for managing problems arising from the pandemic-induced unfavorable working conditions. This study analyzes how this information affects workers' attitudes, highlighting the role of equity as a mediator in this process.